#! /bin/sh # This is a shell archive. Remove anything before this line, then feed it # into a shell via "sh file" or similar. To overwrite existing files, # type "sh file -c". # The tool that generated this appeared in the comp.sources.unix newsgroup; # send mail to comp-sources-unix@uunet.uu.net if you want that tool. # If this archive is complete, you will see the following message at the end: # "End of shell archive." # Contents: readme.doc Makefile ansi.h tfd.dat bird.dat dros.dat # format format.txt interp interp.txt mammal.dat program program.txt # running running.txt sample.seq scanl.c scanm.c scans.c signal.c # signal.lst sigref.doc title.c user user.txt usersig.c xenopus.dat # yeast.dat # Wrapped by dxp@trna on Tue Sep 4 10:39:18 1990 PATH=/bin:/usr/bin:/usr/ucb ; export PATH if test -f 'readme.doc' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'readme.doc'\" else echo shar: Extracting \"'readme.doc'\" \(6256 characters\) sed "s/^X//" >'readme.doc' <<'END_OF_FILE' X S I G N A L S C A N X XUNIX USERS SEE UNIX INSTRUCTIONS BELOW FOR UNPACKING, COMPILING... X XFiles included with this program are: XSIGNAL.EXE(starts the program) XSCANS.EXE (used by program) XSCANM.EXE ("") XSCANL.EXE ("") XUSERSIG.EXE ("") XTITLE.EXE ("") XMAMMAL.DAT (Signal file for mammals) XBIRD.DAT (etc.... XXENOPUS.DAT ... XDROS.DAT ... XYEAST.DAT .....yeast) XTFD.DAT (Ghosh's Trans. factor database, Sept. 1990) XPROGRAM XFORMAT XRUNNING XINTERP XUSER XFORMAT.TXT XRUNNING.TXT XINTERP.TXT XPROGRAM.TXT XUSER.TXT XSIGREF.DOC (reference list for signals) XSAMPLE.SEQ (sample sequece file) XREADME.DOC (this file) X XPrint out all *.DAT & SIGREF.DOC files for review and look at HELP in Xprogram menu for program information before taking any results seriously. X X XStart program by typing SIGNAL X XPROGRAM NOTES: VERSION 1.00 X X_____________________________________________________________________________ XNote that if you do not specify a SAVE file, the program will attempt to run, Xbut when an internal buffer fills up and attempts to write to a nonspecified Xfile, it will lock up the computer and keyboard, and you will have to reboot. X_____________________________________________________________________________ XThere are many more signals in mammal.dat file than the others, this is Xbecause this is the area where most signal research has been done. If Xyou want to search Dros. sequences, you may also want to search with Mammalian Xsignals, since there may be signals in the mamml.dat file that Xare also significant in Dros. sequences. Same with other organisms. X_____________________________________________________________________________ XKeep in mind that many of the signal finds may mean very little, while some Xmay be very important. Some signals were included here only for the sake of Xcompleteness, such as the v-myb binding sequence. While v-myb has been shown Xto bind a particular sequence, it has not been demonstrated that this sequence Xhas any regulatory significance. X_____________________________________________________________________________ XRELEASE NOTES VERSION 1.01 X X-Fixed problem with mapping of elements on extreme right side of sequence X lines. Version 1.00 did not map those elements correctly. X X-Updated the signal databases. X X-There is now an ANSI C compatible source code available for anyone who X wants to port over this program to bigger and faster machines, I will send X it upon request. X X-There is now a version of this program that has been ported over to UNIX X on Sun-3 and Sun-4 machines, I will send a copy on request. I also have X versions that can run on a VAX machine running UNIX or CRAY's running X under UNICOS. X X-Note that I have moved from Duke Univ. to Los Alamos National Lab, my new X address is in user information in the HELP part of the program. X X-I removed the splice site consensus signals from the mammal.dat database X because they are highly inaccurate in predicting splice sites, and there X are better programs available for predicting them. X X-Increased maximum sequence size from 5000 to 10,000 bps. X_____________________________________________________________________________ XUNIX VERSION NOTES: X X-the UNIX version is sent in 'shar' format. Unpack this by X removing mail header lines, and type "sh signal.shar". This X will unpack the files. Next type "make", and all of the X source will be compiled. Type "signal" to begin. A sample X sequence is included to demonstrate the sequence file format, X and can be used to try out the program for the first time, it X is called "sample.seq". X X-maximum sequence length is 100,000 bp X X-this version runs best on VT-100/220 etc. screens, and may not do X so well on SUN screens. The reason is the uses of some ansi X features used in text screen graphics that are not interpreted X well by Sunview or Openwindows. X X-Many screen types may not show the intensity of the first X letter of a selection, ie., "M"ammal where "M" is bright, X this is to indicate that you are to press "M" to select X mammal, not to type the word mammal. To make any selection X throughout the program, always press the first letter of the X selection (case insensative) followed by a return. X X-please let me know any problems you have with this software, X any any bug to fix or suggestions for improvement. X X-the next update of the database will probably be sometime early X next year ('91). Since most of my work involves developing X programs for eukaryotic POL II promoter analysis and X recognition, I don't have much time to spend on updating the X database, but will do what I can. X X-let me know if this program is of any use to you, and I would X appreciate an acknowledgment if you use this program successfully X in your research. I have submitted a paper on this and will X give the citation here if it is accepted. X X-I am not responsible for my spelling. Or any of the years X of research you may put into looking into anything suggested X by SIGNAL SCAN results. X X-Good luck! X_____________________________________________________________________________ XVERSION 1.02 X X-Added David Ghosh's Transcriptional Factor Database SITES data X (NAR 18.7: 1749-1756). Data and reformatting kindly provided by David Ghosh. X X-Note that the TFD.DAT file X differs slightly from the standard SIGNAL SCAN data files in that the X reference number refers to a MEDLINE reference number. X X-Note that TFD.DAT is about 10x larger than MAMMAL.DAT, hence will slow X execution time down proprortionatly. I hope to speed this up some in the X future. X X-The TFD data is not incorperated in any of the other database files at the X present. In the future, I will probably rely heavily upon Ghosh's TFD X for the source of data to be gradually incorperated into the MAMMAL.DAT X and other data files, but for now TFD data is independant of other data X files. This means that if you want to find factors binding a mammalian X sequence, I would recommend running the sequence through both the X MAMMAL.DAT and TFD.DAT databases. X X-The TFD database is not partitioned by species, but is all inclusive. X X____________________________________________________________________________ END_OF_FILE if test 6256 -ne `wc -c <'readme.doc'`; then echo shar: \"'readme.doc'\" unpacked with wrong size! fi # end of 'readme.doc' fi if test -f 'Makefile' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'Makefile'\" else echo shar: Extracting \"'Makefile'\" \(290 characters\) sed "s/^X//" >'Makefile' <<'END_OF_FILE' Xall:signal title scans scanl scanm usersig X Xsignal:signal.c X cc -O -o signal signal.c X Xtitle:title.c X cc -O -o title title.c X Xscans:scans.c X cc -O -o scans scans.c X Xscanl:scanl.c X cc -O -o scanl scanl.c X Xscanm:scanm.c X cc -O -o scanm scanm.c X Xusersig:usersig.c X cc -O -o usersig usersig.c X END_OF_FILE if test 290 -ne `wc -c <'Makefile'`; then echo shar: \"'Makefile'\" unpacked with wrong size! fi # end of 'Makefile' fi if test -f 'ansi.h' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ansi.h'\" else echo shar: Extracting \"'ansi.h'\" \(1110 characters\) sed "s/^X//" >'ansi.h' <<'END_OF_FILE' X#define CLR puts("\033[2J") /* clear screen */ X#define CLR_LINE puts("\033[K") /* clear line */ X#define CUR_MOVE(r,c) printf("\033[%d;%dH",r,c) /* move cursor to r,c */ X#define CUR_UP(x) printf("\033[%dA",x) /* move cursor up x rows */ X#define CUR_DOWN(x) printf("\033[%dB",x) /* move cursor down x rows */ X#define CUR_RIGHT(x) printf("\033[%dC",x) /* move cursor right x col. */ X#define CUR_LEFT(x) printf("\033[%dD",x) /* move cursor left x col. */ X#define CUR_SAVE puts("\033[s") /* saves cursor position */ X#define CUR_RESTORE puts("\033[u") /* restores cursor position */ X X#define fCUR_MOVE(y,r,c) fprintf(y, "\033[%d;%dH",r,c) /* move cursor to r,c */ X#define fCUR_UP(y,x) fprintf(y, "\033[%dA",x) /* move cursor up x rows */ X#define fCUR_DOWN(y,x) fprintf(y, "\033[%dB",x) /* move cursor down x rows */ X#define fCUR_RIGHT(y,x) fprintf(y, "\033[%dC",x) /* move cursor right x col. */ X#define fCUR_LEFT(y,x) fprintf(y, "\033[%dD",x) /* move cursor left x col. */ X#define fCUR_SAVE(y) fputs(y, "\033[s") /* saves cursor position */ X#define fCUR_RESTORE(y) fputs(y, "\033[u") /* restores cursor position */ END_OF_FILE if test 1110 -ne `wc -c <'ansi.h'`; then echo shar: \"'ansi.h'\" unpacked with wrong size! fi # end of 'ansi.h' fi if test -f 'tfd.dat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'tfd.dat'\" else echo shar: Extracting \"'tfd.dat'\" \(80388 characters\) sed "s/^X//" >'tfd.dat' <<'END_OF_FILE' XUASg CGGAAGACTCTCCTCCG 17 87131096 XHSE CTNGAANNCTTNAG 14 83232871 XZDNA_CS GCGTGTGCA 9 83219298 XARE.1 ATGACTCAT 9 XAd5I/EIA AGAAGTGAAA 10 XAd5II/EIA AGTAAGATTTG 11 XAdE2 ACCGNNNNCGGT 12 87090404 XAlb_DEI ATTTTGTAAT 10 XAlb_DEII TTTTTGGCAAGGAT 14 XAlb_DEIII GCAAGGGATTTAGTT 15 XAlb_PEI TGGTTAATGGATCTACAGT 19 XE2-RS ACCNNNNNNGGT 12 XCACA CACACACACA 10 Xdc_box TSATTTGCAT 10 XGALV_E AGAAATAGATGAGTCAACAG 20 XGCRE TGACTC 6 86079487 XGH_prom GANNTTNNAAATTAT 15 XGRE.1 AGAACAGATG 10 XGTI GGTGTGGAAGT 11 XGTII GCTGTGGAATGT 12 XH2KBI TGGGGATTCCCCA 13 88038861 XH4siteII CTGGTCCG 8 87234336 XHCMV2 CCCCATTGACGTCAATGGG 19 85176976 XHCMVIE TGACGTGTTT 10 XHIV_enh GGGACTTTCC 10 XHSVIE TAATGARAT 9 84216449 XHSV_CS3 AGCGTTCGCACTTCGTCC 18 XHSVori_CS2 CGTTCGCACTT 11 XHSVtk ATTGGCGAAT 10 XIg_E1 AGTCAAGATGGCCGA 15 XIg_E3 AGGTCATGTGGCAAC 15 XIg_cd ATGCAAATNA 10 84295592 XIg_core GCCAGGTGGC 10 85137896 XIg_dc TGATTTGCAT 10 84295592 XIg_pd TGCAGCTGTGNCNAN 15 84295592 XKAPPA GGGGGACTTTCC 12 86298399 XLVa_RS GAACAG 6 87172777 XLVb_RS CAGGATA 7 87172777 XLVc_RS CCTGC 5 87172777 XMRE_CS1 TGCRCYCG 8 XNFI_CS1 TGGMNNNNNGCCAA 14 XNFI_CS2 TGGNNNNNNNGCCA 14 XNFI_CS3 TGGNNNNNNGCCA 13 86220117 XNFkB.1 CAGAGGGAGTTTCCGAGAGC 20 XNFkB.2 ATGGGTTTCCTA 12 XNFkE2 GTCCCATGATGGTTA 15 XOCTA1.1 ATTTGCAT 8 86092241 XOCTA1.2 ATTTGCAT 8 XOCTA1.3 ATTTGCAT 8 XOCTA2.1 CAGGTGGC 8 85090419 XOCTA3 ATGCAAAT 8 84194064 XPE RGTTARTNNTYNNC 14 XPE-a ACTGACCGC 9 87275827 XPE-a GACCGCA 7 87275827 XPRL_prom CCTGAWWA 8 XR/Prolac_I GCTGAAATTAATCAAAA 17 XR/Prolac_II TCCTTCTTTCTG 12 XSCMVIE ACGGTAAATGGCCC 14 XSV40_P ACTGATTAACT 11 XSV40-SPHII AAGTATGCAAAG 12 XSV40-core GTGGWWWGGTCCCCA 15 83119921 XSP1_CS1 KGGGCGGRRY 10 85296323 XSRE.1 ATCYYATTWTCTGKTTGTA 19 82272313 XTAATGARAT TAATGARAT 9 XTGGCCA_RS YTGGCANNNTGCCAR 15 85215598 XVP5_Prom AGGGCCATCTTGAA 14 X|TIF TAATGARAT 9 X|GLOBIN CCACACCC 8 86179883 X|IFN_CS AAWAANGAAAGGR 13 85176975 XcAMP_RE TGACGTCA 8 87231855 XdGHF1 AGCTTCTAAATTATCCAT 18 XhmtIIa AGTACACTTTGT 12 84168159 XoriP_CS TAGCATATGCTA 12 XpGHF1 CCATGCATAAATGTACACAG 20 XpolII_term ATCRAAWTAGWAAKAGCAAT 20 86232546 XtopoI_RS ARACTTAGATAAAWWW 16 85176978 XMRE_CS2 STGCGCCCGGCC 12 XMRE_CS4 YKCGCCCGGCYC 12 XNFkB_CS1 GGGGACTTTCC 11 XPE_EF-C AGTTGC 6 XRSVEFII_RS TCTTATGCAATACTCTTGTA 20 XRSVEFI__RS ACCGTGCATGCCGATTGGTG 20 XcfosSRE GATGTCC 7 XcfosSRE.2 GATGTCCATATTAGGACAT 19 XTATAbox TATAAA 6 87117506 XCAAT GGYCAATCT 9 87117506 XFSE2.1 GAGAGGA 7 XFSE2.2 ACTCAGAGGAAAA 13 XAD_MLP GGCCACGTGACC 12 88112839 XFSE1 GGGWCTGGTCAKG 13 87215947 XAP2_CS1 TCCCCANGCC 10 88027009 XAP2_CS2 CCGCCCGCG 9 XAP3.1 GGTGGWWWGT 10 88014240 XAP4_CS YCAGCTGYGG 10 88189275 XCAAT.1 AACCAAT 7 88165047 XCAAT.2 AGCCACT 7 88165047 XCAAT.3 AGCCAAT 7 88165047 XAPF_CS RGTTARTNNTYNNC 14 XUAS2 CACCAAT 7 XGRE_CS2 ACANNNTGTTCT 12 XURS2 CACGAAAA 8 87102888 XpolI_term AGGTCGACCAGWWNTCCG 18 XEiv_prom GTKACGW 7 XADH2_prom TCTCCAACTTATAAGTTGGAGA 22 XAC1_rec CAATTAAA 8 XCUP1_prom TCTTTTTGCT 10 X|-globin GATAAG 6 XOcta1.4 ATGCAAAG 8 88112794 XOcta2.2 ATGCATCT 8 88112794 XG-string GGGCGG 6 XHNF-1_RS GTTAATNATTAAT 13 XHDII_rec TCAATTAAATGR 12 XB1-A/B AAAWWGGAAWYG 12 XB2_rec TCCTATCA 8 XTyBF_RS GTCATCATAGACG 13 88302168 XSRE.2(pal) TGTTCT 6 XICS_core AGTTTCACTTC 11 XP1_Op72 ATTGCTCTAATAAATTT 17 XPAL TTCCTAATTAGGAA 14 XEBP20_CS1 TKNNGYAAK 9 88056262 XAmy_prom TGTTCT 6 XNF-GMa GAGATTCCAC 10 Xcytokine-2 TCAGGTA 7 XERE GGTCANNNTGACC 13 XCoup_box GGGTCAAAGG 10 XMHCemb GTGTCAGTCA 10 XKeratin_pr TTTGGCTT 8 XTATA TATAAT 6 XNod_box ATCCAAACAATCRATTTTACCAATC 25 XG-box SGGGTGKGTT 10 XGH0 ACCGACCG 8 XGH1 TCTGTCTG 8 XH2 ACCGACTG 8 XGHN CTCGAGTACGAWCYGWYCGTCGGTA 25 XIR TTATCCAAAACCTCGGTTTACAGGA 25 XEIIF_RS GACGTAGTTTTCGCG 15 XtopoII_CS GTNWAYATTNATNNR 15 XTATA TATAAA 6 XMHCIIpromA YAGNWAACAGATGA 14 XMHCIIpromB CTGATTGG 8 XARE.2 TKAGTCA 7 87215938 XCRE.2 KWCGTCA 7 XNFI_CS4 TGGCTNNNAGCCAA 14 XSP1_CS2 GGGCGG 6 86315855 XE2F_CS.1 TTTCGCGC 8 88004418 XAP3.2 GGGTGTGGAAAG 12 XEBP20_CS2 TGTGGWWWGCCAAT 14 XAP5_site CTGTGGAATG 10 87201903 XEF-C.2 GTTGCNNGGCAAC 13 87041493 XE2A_prom TGGGAATT 8 88243009 XE4_prom GGAAGTG 7 XEIIaE_prom.2 AGATGACGTA 10 XHMR WTTTATRTTTW 11 Xen_RS TCAATTATTAT 11 Xes_RS TCAGCACCG 9 XSomatostat TGACGTCA 8 XLympk_cons GRGRTTYCAY 10 XOval_prom GTGTCAAAGCTTC 13 XEGFR_prom CCCAGACCGGACGACAG 17 XMHCIIA.2 CCCAGCGAGTGATG 14 XMHCIIB.2 CCCATTGGTT 10 XMT/G-box GSGGGSCGKGTGCA 14 88225998 XMRE_CS3 CTNTCCRCNCGGCCC 15 XIL2/Bsite TAATATGTAAAACATTTT 18 XRev_CAAT ATTGG 5 XEa_boxB YNNTKCTGATTGGYT 15 XEa_boxA CCTAGCAACAGATG 14 XEa_boxH GGACCTG 7 XISRE YAGTTCWYTTTYCC 14 XARS_CS WTTTATRTTTW 11 Xdc_box.2 TNATTTGCAT 10 XApoCIIIp1 CTCAGGCCCT 10 XApoCIIIp2 GGTGACCTT 9 XApoCIII- GAGTTGGGAAATCCCT 16 XApoCIIId CCCCACTGAGGAACC 15 Xcytomeg18 MCTAACGGGACTTTCCAA 18 Xcytomeg19 CCCCATTGACGTCAATGGG 19 XAP2_CS3 CCSCRGGC 8 87301729 XPRDI GAGAAGTGAAAGTG 14 XPRDII GTGGGAAATTCC 12 XNRCI AATTCCTCTGAATAGAGAGAGGAC 24 XATF_CS GTGACGTMR 9 XTCRb_prom AGTGAYRTCA 10 XAp1-E3 GTTAGTCAT 9 XAp1-SV ATTAGTCAG 9 XAp1-Col ATGAGTCAG 9 XHIS-wt AAGAGTCAT 9 XHIS168 AAGCGTCAT 9 XGH-CSE TAAATTA 7 88227987 XGH-CSE2 AATAAAT 7 88227987 XGH-TRE AAAGGCGG 8 88227987 XCYP1 TAATAGCGA 9 XUAS1A TTTCACCGATCTTTCC 16 88302133 XUAS0 CTAATAGCGATAATAGCGAGGG 22 88302133 XUAS1B TCATCGTCCGTAAACCCCGGCCA 23 88302133 XSlp/FPI AAAGTCTCTGGATGATGCAACCCTC 25 88302143 XSP-D CCTCTAAGAGACAG 14 88302154 XSP-D CCTCTAAGAGACAG 14 88302154 XSP-E GACAGTCAT 9 88302154 XCDEI ATCACGTG 8 88302163 XCDEIII TGWTWTGNNTTCCGAANNNNNAAA 24 88302163 XCEN6 AGTTTTTGCTTTCCGAAGATGTAAA 25 88302163 XAPRT_cons GCCCCRCC 8 88302164 XAPRT-C GCCCCACC 8 88302164 XAPRT-M GCCCCGCC 8 88302164 XAPRT-H GCCCCACC 8 88302164 XCYC7-H2 GTTAGACGTTTCAGCTTCCAAAACA 25 88302165 XIgHuE1 GGCCATCTTG 10 88112808 XIgHuE2 TGCCAGCTGC 10 88112808 XIgHuE3 TGCCACATGA 10 88112808 XNir_box CGCCATCTGC 10 88302174 XGAGA_RS MGAGAGAGC 9 88223364 XZESTE_RS YGAGYC 6 88223364 XHIG1_prom TATTTTAGGAAGCAAA 16 88223366 XIL2R_RS GGGGAATCTCCC 12 88223375 XSal_box AGGTCGACCAGKK 13 XCArG_box CCWWWWWWGG 10 XIgHN1 GCAGGTCATGTGGCAAGG 18 87004545 XIgHN2 ACTAGGTAAACTTGTAGCTGTGG 23 87004545 XIgHN3 TGAAACACT 9 87004545 XIgHN4 AAAGTCCAG 9 87004545 XIgHN5 TGGGTAATTTGCATTTCTA 19 87004545 XIgLN1 GCAGGTCATGTGGCAAGG 18 87004545 XIgLN2 GGGGAAGGGAAAATAAAACC 20 87004545 XIgLN3 ACTAGGTAAACTTGTAGCTGTGGTT 25 87004545 XIgLN5 TGGGTAATTTGCATTTCTAAAATAA 25 87004545 XIgHC2 TTGAAACA 8 87004545 XIgHC3 CCACCA 6 87004545 XIgHC4 ACCTGGGTAATTTGCATTTCTA 22 87004545 XIgLC1 TTTTCCCTTCCCCAAATAGCCTTGC 25 87004545 XLF-A1_RS TGRMCC 6 89005060 XLF-A2_RS TGGTTAAT 8 89005060 XrPrl.A CTGATTA 7 89005061 XrPrl.B TGAAGGTGTCGAAGGT 16 89005061 XHAP1 AACCTCCGTTATCTCCATT 19 89005071 XNFI.1 ACATTCTCCTTGCCAAG 17 88228086 XLam_B2_US CCCKCCCWCCT 11 88228071 XApoE_SRE CCTCTCCAGATTACATTCATC 21 88228059 XApoE_B1 SCCCACCTC 9 88228059 XApoE_B2 SSCCCCAGNNTC 12 88228059 XApoE_A CTCCCYCTGYCC 12 88228059 XCDF1_RS CTAAATAC 8 88228057 XEBP20_CS3 TCNTACTC 8 88234517 XEBP20-TTRS2 TAATACTC 8 88234517 XEBP20-TTRS3 TCTTACTC 8 88234517 XEBP20-ATsA ACCTACTC 8 88234517 XEBP20-ATsC1 TAAGACTC 8 88234517 XEBP20-ATsC2 TCTTAAGC 8 88234517 XEBP20-SVC TTCCACAC 8 88234517 XEBP20-ADEI1 TCCTACCC 8 88234517 XEBP20-ADEI2 TCATACCA 8 88234517 XEBP20-SV GTTAGGGTGTGGAAAGTCCC 20 88056262 XEBP20-MSV AGGATATCTGTGGTAAGCA 19 88056262 XEBP20-PY AGTGTGGTTTTGCAAGAGGAA 21 88056262 XIEF1_RS GCCATCTG 8 88247995 XNFkB_CS2 RGGGRMTYYCC 11 88261502 XNFkB-HIV GGGGACTTTCC 11 88261502 XNFkB-b2m AGGGACTTTCC 11 88261502 XNFkB-HIgk GGGGGATTTCC 11 88261502 XNFkB-H2TFI GGGGAATCCCC 11 88261502 XNFkB-IL2Ra GGGGAATCTCC 11 88261502 XNFI.2 GCCAATC 7 88065503 XNFI.3 TGGATTGAAGCCAA 14 84016017 XNFI.4 TGGGCACAGTGCCAA 15 85213500 XNFI.5 TGGCTTTGGGCCAA 14 85213500 XNFI.6 TGGATTTGTGCCAA 14 85213500 XNFI-cmycII1 TGGAAGGCAGCCAA 14 84205672 XNFI-cmycII2 TGGAAGGTATCCAA 14 84205672 XNFI.7 TGGCACTATGCCAC 14 85213500 XNFI.8 TGGGCAGATTGCCAA 15 85213500 XNFI.9 TGGCAAGCTGTCAA 14 85213500 XNFI-wt TTGGATTGAAGGCCAA 16 86148473 XNFI.10 TGGCACTGGGCCAA 14 85163737 XNFI.11 TGGCACATGGCCAA 14 86274639 XNFI.12 TGGCTAATGGCCAA 14 86274639 XNFI.13 TGGCCAATAGCCAA 14 86274639 XNFI.14 TGGACATGAGCCAA 14 86274639 XNFI.15 TGGCTATATGCCAA 14 86274639 XNFI.16 TTGGATTGAAGCCAAT 16 85269618 XNFI-CSLa1,1 CATCCGTGGCTGGAGCCAAAAGTG 24 84221360 XNFI.17 ATTTTGGATTGAAGCCAATATGA 23 87144259 XCTF GCCAATGA 8 85282613 XNFI-tkII ACCCCGCCCA 10 85282613 XNFI.18 TGGATTGAAGCCAATA 16 85284942 XCRE-Ga TGACGTCA 8 88257120 XGa-URE ACTGGATTCCCAACTTTG 18 88257120 XIL2_CS ASAAASGAGGAAAAACTG 18 86272087 XLysHREI CAGAGAACACAGG 13 88328995 XLysHREII TTTATGTACAGGG 13 88328995 XLysHREIII AGAAGACTTTCCATTCTGGCCACA 24 88328995 XLysHREIV CCCAGTTTGTACAGTTCTGGCACTT 25 88328995 XLysHREV AGGCCGTGATCCAAGGAGCAGAAGT 25 88328995 XLFA1_RS CAGATCCCAGCCAGTGGACTTAGCC 25 88328996 XEBP1_RS GGGACTTTCC 10 88329000 XGRF1_RS ATAACGTTTTTTGGGTAGTTGGAAC 25 88329012 XCabE_PRE ACCGGCCCACCT 12 88328979 XSP1-MTIIA GGGGCGGGGC 10 XSP1-IE3/34 TGGGCGGGGC 10 XSP1-SV3/5 TGGGCGGAGT 10 XSP1-DHFR.1 GGGGCGGAGC 10 XSP1-IE3/1 GGGGCGGGGG 10 XSP1-IE3/2 GGGGCGGGGT 10 XSP1-TK/2 TGGGCGGGGT 10 XSP1-SV/2 TGGGCGGAAC 10 XSP1-SV/4 GGGGCGGGAT 10 XSP1-SV/6 GGGGCGGGAC 10 XSP1-SV/1 GGGGCGGAGA 10 XSP1-TK/1 GGGGCGGCGC 10 XE4-160R.O CGTTACGTCA 10 88275073 XE4-45R.D CGTTACGTCA 10 88275073 XITRN63.O CGCCACGTCA 10 88275073 XETFA AACTACGTCA 10 88275073 XAAVN.160.O ATTCACGTCA 10 88275073 XAAVN.170.D AATTACGTCA 10 88275073 XAAVN.210.D GGTCACGTGA 10 88275073 XPEPCK-80.D CCTTACGTCA 10 88275073 XETFA.2 YYACGTCA 8 88275073 XETFA.3 TGACGTRR 8 88275073 XETF_RS1 CAGCCCCCGGCGCAG 15 88276890 XETF_RS2 CCCCCGGC 8 88276890 XAP2_CS4 YCSCCMNSSS 10 88027009 XTfPRI CGGGAGGTCAAAGATTGCGC 20 88273108 XTfPRII GGGCGATTGGGCAACCCGGC 20 88273108 XTfDRI TCTTTGACCTTGAGCCCAGCT 21 88273108 XTfCR GTGCTGGACTCCTTCCACTCGCGG 24 88273108 XAd_DPS GTGGCCGCGTCCATCTGGTCAGAAA 25 88273141 Xb/e_E2 AGTCTTGATAGCAAAA 16 88320366 Xp_P1 CAGCAAGATAAGGGCT 16 88320366 Xbh_P1 AGGAAAGATAGCAAAT 16 88320366 X|-p_US GGATAAGATAAGGCCG 16 88320366 X|_P CAAGGAGATAAGGGTC 16 88320366 X|A_E1 GGCCGTGATAAGAGCC 16 88320366 X|A_E2 GTGGCTGATAAAGAGC 16 88320366 X|A_E3 GCAGCAGATAGCCTCG 16 88320366 XPEA1_RS TGACTAA 7 88320339 XPEA2_RS GACCGCA 7 88320339 XPEA3_RS AGGAAG 6 88320339 XPEB1_RS CAGAGGGCAGTGTG 14 88320339 XEF-C_RS GTTGCTAGGCAAC 13 88320339 XXRE_CS1 CACGCW 6 88320348 XXRE_CS2 GNNSMNGNNCNTNTNCCGCWA 21 88320343 XXRE1 CCTCCAGGCTCTTCTCACGCAACTC 25 88320343 XXRE2 CGGTCCCAGTGCTGTCACGCTAGCT 25 88320343 XEivF_CS GTKAGGT 7 89006221 XICS AGTTTCTCCTCT 12 88320348 XICS-H2Ld AGTTTCACTTCT 12 88320348 XICS-H2Kb AGTTTCACTTCT 12 88320348 XICS-H2Dd AGTTTCACTTCT 12 88320348 XICS-b2m AGTTTCATGTTC 12 88320348 XICS-HLADR AGTTTCTCCTCT 12 88320348 XICS-HLAA3 AGTTTCTTTTCT 12 88320348 XICS-MTII AGTTTCTCCTCT 12 88320348 XICS-FacB AGTTTCTGTTTC 12 88320348 XICS-ISG15 AGTTTCGGTTTC 12 88320348 XICS-ISG54 AGTTTCACTTTC 12 88320348 XICS-6-16 AGTTTCATTTTC 12 88320348 XICS-os GGTTTCGTTTCC 12 88320348 XICS_CS AGTTTCNNYTYY 12 88320348 XAPF-alb1 TGGTTAATGATCTACAG 17 89006221 XAPF-alb2 TGGTTAATGATCTACAG 17 89006221 XAPF-alb3 TAGTTAATAATCTACAA 17 89006221 XAPF-alb4 CAGGTAATGTTTTACAG 17 89006221 XAPF-alb5 AGGTTAATAATTTTCCA 17 89006221 XAPF-alb6 AGGTTAATCATTTTCCA 17 89006221 XAPF-AFP1 AGGTTACTAGTTAACAG 17 89006221 XAPF-AFP2 AGGTTACTAGTTAACAG 17 89006221 XAPF-AFP3 AGGTTACTAGTTAACAG 17 89006221 XAPF-AT TGGTTAATATTCACCAG 17 89006221 XAPF-FIB1 TAGTTAATATTTGACAG 17 89006221 XAPF-FIB2 AGGTTAATCATCACCCT 17 89006221 XAPF-PK TGGTTATACTTTAACCA 17 89006221 XAPF-HG CTGTTAAGAGTTGAGCT 17 89006221 XAPF_CS RGTTAMTNNTYNNCM 15 89006221 XEBP1_RS GTGGAAAGTCCCC 13 89006222 XCOUP-oval TGACCTTTGACAC 13 89030640 XCOUP-VLDL GGACCTTTGACCC 13 89030640 XUAS1.3 TGGCCGGGGTTTACGGACGATGA 23 87159552 XUAS1.1 GGCCGGGGTTTAC 13 87159552 XUAS1.2 GATGACGA 8 87159552 XTFIID-EIIa TACAAA 6 88315059 XUCE.1 GTCCGT 6 88321668 XUCE.2 GGCCG 5 88321668 XUCE.3 GTCCGTGTCGNNNNNNNNNTGGGCC 25 88321668 XrRNA_UScor CTCCGAGTCGNNNNNNTGGGCCGCC 25 88321668 XNFBK.1 TGGAATGCAGCCAAA 15 88300893 XNFBK.2 GGGAATGCAGCCAAA 15 88300893 XNFBK.3 TGGGCAGCMGCCAGT 15 88300893 XNFBK.4 TGGAAACTGGCCAAA 15 88300893 XNFBK.5 TGGCTGCTTTCCACT 15 88300893 XNFBK.6 TGAAACCATGCCAAA 15 88300893 XNFBK.7 TGGCCTTGTCCCCAG 15 88300893 XNFBK_CS TGGAAWSYWGCCAAA 15 88300893 XNFIII-Ad2 AATATGATAATGAGG 15 88300856 XNFIII-Ad4 AATATGCAAATAAGG 15 88300856 XNFIII-SA7 AATATGCTAATGAGG 15 88300856 XNFIII-Ad12 AATATTAAAATGAAG 15 88300856 XNFIII-Ad40 AATATGATAATGAGG 15 88300856 XNFIII-Ad41 AATATGATAATGAGT 15 88300856 XHNFI-|Fib GACAAGGGTGATGATTAACCTAGTT 25 88042798 XHNFI-|Fib AACAAACTGTCAAATATTAACTAAA 25 88042798 XHNFI-|1AT CCTTGGTTAATATTCACCAGCAGCC 25 88042798 XNF-Y TKCTGATTGGYTMM 14 87301730 X|1AT-Hapt TGGACACAGG 10 88054974 X|1AT-CS TGTGGTTT 8 88054974 X|1AT-RBP CTGAGCCAGG 10 88054974 XNFY-E| ATTTTTCTGATTGGTTAAAAGT 22 88015594 XAP1-Col.2 TGAGTCAG 8 87215937 XAP1-strom TGAGTCAG 8 87215937 XAP1-hmtIIa TGACTCAG 8 87215937 XAP1-polyom TGCGTCAG 8 87215937 XAP1-polyom TTAGTCAC 8 87215937 XAP1-IL2 TCAGTCAG 8 87215937 XAP1_CS TGAGTCAG 8 87215937 XNF-E1_CS MYWATCWY 8 89053047 XNF-E1.1 TGCTAATCAT 10 89053047 XNF-E1.2 CTTATCTT 8 89053047 XNF-E1.9 AAGTATCACT 10 89053047 XNF-E1.3 CTATCA 6 89053047 XNF-E1.4 TTATCTC 7 89053047 XNF-E1.5 TATCTT 6 89053047 XNF-E1.6 TATCTC 6 89053047 XNF-E1.7 TCATCAC 7 89053047 XNF-E1.8 CCAATCT 7 89053047 XLBP-1_RS WCTRG 5 89053048 XIL2R|-kB GGGGAATCTCCC 12 88336901 XCRE.1 CGTCA 5 88320498 XXY_CS.1 CCTAGMRACWGATG 14 89039821 XXY_CS.2 TKCTGATTGGYTMM 14 89039821 XCArG_CS CCAWATWWGG 10 89039835 XCArG-hcact CCAAATAAGG 10 89039835 XCArG-fos CCATATTAGG 10 89039835 XCArG-xcact CCATATTTGG 10 89039835 XCArG-csact CCAAATATGG 10 89039835 XCArG-hsact CCAAATATGG 10 89039835 XCArG-hs1 CCCAAATATGGCTC 14 89039836 XCArG-hs2 TCCTTCTTTGGTCT 14 89039836 XCArG-hs3 CCATATACGG 10 89039836 XCArG-hc1 CCAAATAAGGC 11 89039836 XCArG-hb1 CCTTTTATGG 10 89039836 XCArG-cs1 CCAAATATGGCGAC 14 89039836 XCArG-sc1 GCCCATATTTGGC 13 89039836 XCArG-fos CCATATTAGG 10 89039836 XS1_HS TCCTCCTCC 9 89039842 XCRE-fos TGCGTCA 7 89039849 XCRE-PE TGCGTCA 7 89039849 XCRE-VIP GACGTCA 7 89039849 XCRE-som TGACGTCA 8 89039849 XENKCRE-1 TGGCGTA 7 89039849 XUASt TCGTTTTGTACGTTTTTCA 19 89039861 XHNF1_RS TGGTTAAT 8 89039864 XMRE_CS5 NTTTGGRCNCGGCYC 15 89039876 XADH2.1 TCTCCAACTT 10 89039889 XADH2.2 TAAGTTGGAGAA 12 89039889 XCREB-Som ACGTCA 6 89017164 XCREB-fos ACGTCA 6 89017164 XCREB-proen GCGTCA 6 89017164 XCREB-hsp70 TCGTCA 6 89017164 XCREB-tyr ACGTCA 6 89017164 XCREB-Fib ACGTCA 6 89017164 XCREB-PEPCK ACGTCA 6 89017164 XCREB-VIP ACGTCA 6 89017164 XCREB-PTH ACGTCA 6 89017164 XCREB-ACG ACGTCA 6 89017164 XCREB-E2a ACGTCA 6 89017164 XCREB-E3 TCGTCA 6 89017164 XCREB-E4 ACGTCA 6 89017164 XCREB-HTLV ACGTCA 6 89017164 XCREB-BLV ACGTCA 6 89017164 XCREB-CMV ACGTCA 6 89017164 XCREB-IAP ACGTCA 6 89017164 XCREB_CS ACGTCA 6 89017164 XNFuE1 AAGATGGC 8 85090419 XCuE2.1 CAGCTGGC 8 85090419 XCuE3.1 CATGTGGC 8 85090419 XCuE4.1 CAGGTGGT 8 85090419 XCuE1.2 GATGGCCG 8 86311318 XCuE3.2 GTCATGTGGCAAG 13 86298399 XCuE4.2 GCAAATTACCCAGGTG 16 86298399 XCuE2.2 GCTGGCAGGAAGCAGGT 17 87004545 XCuE3.3 CATGTGGCAAGG 12 87004545 XIgPE2_RS CCACCAAACCGAAAGTCCAGG 21 87004545 XCuE4.3 CCTGGGTAATTTGCATTTCTAAAAT 25 87133485 XCuE2.3 AGCAGCTGGC 10 87234354 XCuE1.3 TCAAGATGGC 10 87234354 XCuE3.4 GTCATGTGGC 10 87234354 XTEF1-SphI AAGCATGCA 9 88327858 XTEF1-SphII AAGTATGCA 9 88327858 XTEF1-GTIIC TGGAATGTG 9 88327858 XTEF1-GTI* TGGAAAGTC 9 88327858 XTEF1-Pywt TAGAATGTT 9 88327858 XTEF1-PyEC9 TGGAATGTT 9 88327858 XGT-I GGGTGTGG 8 88112821 XERE.cvitII GGTCAGCGTGACC 13 89017230 XGRE.cvitII AGAACACATTGATCC 15 89017230 XDRE.cvitII AGAACATGATGTTCT 15 89017230 X|pol_CS NTGACGTCAN 10 89034198 X|pol_RS GTGACGTCAC 10 89034198 XPUT2_UAS.1 GAAGCCAA 8 89096832 XPUT2_UAS.2 GAAGCCGA 8 89096832 XuEBP-E_CS TNNAKYNNKNNMTNATGA 18 89096871 XHSV/AT GWATCYCATTANCATRC 17 XAT/|0.1 GAAACTCATTACCATAC 17 XAT/|0.2 GAACCCCATTAGCATGC 17 XAT/|0.3 GAATATCATTAGCATGC 17 XAT/|4.1 GCATCTCATTACCGCCC 17 XAT/|4.2 GAATTCCATTATGCACG 17 XAT/|27.1 GTAATTAATTAGCATAT 17 XAT/|27.2 GAGGCCAATTAGCATAT 17 XAT/|47.1 GTTCCTCGTTAGCATGC 17 XAT/|47.2 GTATCTCCTTACCGCCG 17 XAT/|47.3 CACTCCTTTTACCCGGC 17 XAT-SV40 GCATCTCATTAGTCAGC 17 XAT-MSV GAACTGCTTACCACAG 16 XAT-SR_CS ATCYYATTWTCTGKT 15 XAT-|INF AAATCTTTTTCCCTATT 17 XAT-hsp GAATNTTCTAGA 12 XAT-LC GAAGTTTTAT 10 XAT-E1A GCGTTTTATTATTATAG 17 XAT-tk GCTTGTCATTACCACCG 17 XAT-|G AAATCYCATTTGTATGA 17 XAT-Alu AGCTGGGATTACAGRC 16 XCBAR CCAAATAWGG 10 89096827 Xeve TCAATTAAAT 10 89096828 Xeve.2 TCAGCACCG 9 89096828 XPUT2_UAS1 GAATGCCAA 9 89096832 XPUT2_UAS2 GAAGCCGA 8 89096832 XSTE2.1 ATGTACTT 8 89003042 XSTE2.2 ATTTACAT 8 89003042 XSTE6.1 ATGTAATT 8 89003042 XSTE6.2 ATTTACAC 8 89003042 XBAR1.1 ATGTAATT 8 89003042 XBAR1.2 AATTACAT 8 89003042 XMFa1.1 GTGTAATT 8 89003042 XMFa1.2 ATTTACAT 8 89003042 XMFa2.1 ATGTATTT 8 89003042 XMFa2.2 ATTTACAT 8 89003042 XMAT|2_CS1 ATGTAATT 8 89003042 XMAT|2_CS2 ATTTACAT 8 89003042 XMAT-OCTA1 ATGCAAAT 8 89003042 XMAT-OCTA2 ATTTGCAT 8 89003042 XHO/-411 ATGTTATTATTTACAT 16 89003042 XHO/-736 ATGTGAATGAATACAT 16 89003042 XMAT|1 ATGTAGAAAAGTACAT 16 89003042 XMATa1/|2CS ATGTNAATAANTACAT 16 89003042 Xa-actin_US GTCGCC 6 87250597 Xactin_5c__US TATAAAA 7 87172790 Xactin-cyto AAGATGCGGATATTGGCGAT 20 87218526 XAd2MLP_US.1 TGTAGGCCACGTGACCGG 18 XAd2MLP_US.2 GGCCACGTGACC 12 86079486 XAd2MLP_US.3 TATAAA 6 86232615 XAd2MLP_US.4 TATAAAA 7 86079486 XAd2MLP_US.5 TATAAAA 7 86079486 XAdh_US1 GCTGCTGCTGCATCCGTCGACGTCG 25 85228247 XAdh_US2 TACTAATACTAATACTAATACTAA 24 85228247 XAdh_US3 GCAGCGCTGCCGTCGCCGGCTGAGC 25 85228247 XAdh1_US2 CCCCGG 6 87250373 XAdh1_US3 CGTGG 5 87250373 XAdh1_US4 CCCACAGGC 9 87250373 XAdh2_US TCTCCAACTTATAAGTTGGAGA 22 85267691 XAlbumin_US1 GCAAGGGATTTAGTTA 16 87273526 XNFI-albumin TTTTTGGCAAGGAT 14 87273526 XAlbumin_US2 ATTTTGTAAT 10 87273526 XAlbumin_US3 TGGTTAATGATCTACAGTTATTGGT 25 87273526 Xadip-P2_US1 AACATGACTCAGAGGAA 17 87215947 XBPV_En.1 ATCGGTGCACCGAT 14 87147244 XAP2-BPV.3 TTGGGGCTCCCCAA 14 88027009 Xa2(I)coll_US1 CCAAT 5 86278237 XNFI_CS5 TCGNNNNNGCCAA 13 86278237 XAP1-col.3 ATGAGTCAGA 10 87159552 XHAP1-CYC1 TGGCCGGGGTTTACGGACGATGA 23 87159552 XRC2-CYC1.1 GCCGGGGTTTA 11 87159552 XRC1a/RC2-CYC GCCGGGGTTTA 11 86030243 XRC2-CYC1.2 GATGACC 7 87159552 XRC1/RC2-CYC TGACCGA 7 86030243 XCYC7_US1 GCTAATAGCGATAATAGCGAGGG 23 87159543 XCYC7_US2 GCAAGGGGCAAAGACAAAGGCACAC 25 88038880 XSp1-DHFR.2 GGGGCGGAGC 10 86118666 XSp1-DHFR.3 GGGGCGGGGC 10 86118666 XE1a.1 GATGTGGTAAA 11 87174795 XE1a.2 GTTGTAGTAAA 11 87174795 XE2E1a CAATTTTCGCGCGG 14 87175637 XE2F-E1a CCATTTTCGCGGGAA 15 87175637 XEIIaE-CaEI GTGGGATTTCCTT 13 87174795 XEIIaE-CbEI CTCATAATGGCGCT 14 88065522 XEIIaE-T1 AGTCCTTAAGAGTCAG 16 87146375 XEIIa-EF/EP TGGAGATGACGTAGTTT 17 86287364 XEIIaE-BEII TGGAGATGACGTAGT 15 87146375 XE2?-EIIaE1 GACGTAGTTTTCGCGC 16 88065522 XE2F-EIIaE1 TAGTTTTCGCGCTTAAATT 19 87317605 XEIIaE-AEII AAGGGCGC 8 88065522 XE2F-EIIaE1 GAAAGGGCGCGAAACTA 17 88004418 XEIIF-EIIaE1 GCGCGAAA 8 87317605 XEIIaE1_US CCTTAAGAGT 10 87146375 XEIIaE1.2 GTCCTTAAGAGTCAG 15 88065522 XGa/CRFEII GGGGGGATTGGG 12 88040407 XGaEII-late AACCCCCC 8 88040407 XCRFEII-lat ATTGG 5 88040407 XUSF-IIEII TGACGCA 7 88040407 XSp1/CRF-EII CGGGCGGGATTGG 13 88040407 XSp1-EII-lat TGGGCGTGGT 10 88040407 XE4F1-E4 ACGTAACGT 9 87275829 XE4F1-E4 CGTTACGT 8 87275829 XGCAEF-1a/T AACACCCA 8 86135993 XATTTEF-1a ACCCACAC 8 86135993 XSCR-indf CAGTTCCCGTCAATG 15 87147256 Xf-EBP-fos GATGTCCATATTAGGACATC 20 88065484 Xc-fos_SRE GATGTCCATATTAGGACATC 20 87172790 Xc-fos GCGCCACC 8 88065485 Xc-fos_US5 GTGACGT 7 88065485 Xc-fos.1 GATGTCCATATTAGGACATC 20 87089788 Xc-fos.2 AAGCCTGGGGCGTAG 15 87089788 Xc-fos.3 AGAGGGCCTTGGGGCGCTTA 20 87089788 Xc-fos.4 CCAGTTCCGCCCA 13 87089788 XGAL4-depGAL ACTTATAT 8 86220139 XGAL4-GAL1-1.3 CGGATTAGAAGCCGCCG 17 85176930 XGAL4-GAL1-1.2 CGGGTGACAGCCCTCCGA 18 86220139 XGAL4-GAL1-1 AGGAAGACTCTCCTCCG 17 86220139 XGAL4-GAL1-1.4 CGCGCCGCACTGCTCCGAACAAT 23 86220139 XGAL4-GAL1-1.5 TCCTC 5 87115887 XGAL4-GAL1-1.6 TTATC 5 87115887 XGAL4-depGA TTATATATC 9 87115887 XGAL2_US2 CACCGGCGGTCTTTCGTCCGTGC 23 86220139 XGAL4-GAL2.1 TATCGGGGCGGATCACTCCGAAC 23 86220139 XGAL4-GAL7.1 CTTCGGAGCACTGTTGAGCGAAG 23 86220139 XGAL4-GAL7.4 GGCTCAACAGTGCTCCGAAGTAT 23 85113168 XGAL4-GAL7.5 GGCTCAACAGTTGTCCGAGCGCT 23 85113168 XGAL4-GAL80 CGGCGCACTCTCGCCCG 17 86220139 XCTF/NF-1a AGCCAAT 7 87078403 XCBFaA-glob CCAAT 5 87039102 XaD-globin-CS2 CCGTGCGG 8 87257917 XaD-globin-B AAGATAAGG 9 87257917 XaD-globin-A CGGGGCGGGTGTACAG 16 87257917 Xb-globin CCACACCCG 9 87078403 XCTF/NF-1b AGCCAAT 7 87078403 XbA-globin GGGGCGGG 8 85201671 XbA-globin GGATCTGGGCACCTTGCCCTGAGCC 25 85201671 XbA-globin CCAAT 5 85201671 X53-bA-glob GAGGAGGGG 9 85201671 XGR_CS AGAWCAGW 8 86287361 XCAGgrowth- TGGCCTGCGGC 11 87246534 XGH.1 AGGGCACCCACGTGACC 17 87246534 XAP2-GH.1 ATGGCCTGCGGCCAGAGGGCACC 23 88027009 XAP2-GH.2 GACAAGCCAGGGGGCATGATCCC 23 88027009 XGHF-1GH.1 NNNTAAATNNN 11 87246534 XGHF-1aGH NNNTAAATNNN 11 87246534 XGHF-1GH.2 NNNTAAATNNN 11 87246534 XGRGH GGCACAATGTGTCCT 15 85140164 XT3rec-GH AGGTAAGATCAGGGGACG 18 87289666 XGC2-GH-CS GAGCTTCTAAATTATCCATCAGCAC 25 87172787 XHBVenh.1 GGGTTATGTCATTGGATGTT 20 88004398 XHBVenh.2 CCTATTGATTGGAAAGTATG 20 88004398 X60-HBVenh TTTACACAATGTGGTTATCC 20 88004398 XEF-C?HBVen TGTTTGCT 8 88004398 XGCN4-HIS3.1 TGACGA 6 87041486 XGCN4-HIS3.2 GAGTCA 6 87041486 XGCN4-HIS3.3 TAGTCAGGGAAGTCA 15 87041486 XGCN4-HIS3.4 TTACTC 6 87041486 XGCN4-HIS TGACTC 6 87041486 XGCN4-HIS3.5 TGACTC 6 86079487 XGCN4-HIS4.1 TGACTC 6 87041486 XHIS4_RS TTGCTAAACCGATGCACAGTGACTC 25 87041486 XGCN4-HIS4.2 TGACTC 6 87041486 XGCN4-HIS4.3 CAGTCA 6 87041486 XGCN4-HIS4.4 TGACTA 6 87041486 XhistoneH2 ATTTGCAT 8 86313585 XOBF-histone ATTTGCAT 8 87273497 XCBFhistone ATTGG 5 87273497 XCDF-H2B1 ATTGG 5 87273497 XOBF-H2B1 ATTTGCAT 8 87273497 XB-factorhi TATAAGTA 8 84106841 XH4TF-1hist GATTTC 6 87016923 XH4TF-2hist GGTCC 5 87016923 Xhistone_H4.1 AAAAGAAATGACGAAATGTCGAGAG 25 87234336 Xhistone_H4.2 CTTTCGGTTTTCAATCTGGTCCGAT 25 87234336 XSp1-HIV-1.1 GAGGCGTGGG 10 86179897 XSp1-HIV-1.2 TGGGCGGGAC 10 86179897 XSp1-HIV-1.3 GGGGAGTGGC 10 86179897 XHMGCoAred_FP1 CTTGCTGGCGCCCCTCACGGCTCAG 25 87231868 XHMGCoAred_FP2.1 TGCTGGAACTCGACCAGCTATTGGT 25 87231868 XHMGCoAred_FP3 GTTCTCCGCCCGGGTGCGAGCAGTG 25 87231868 XHMGCoAred_FP5 GGTGATTGGCTAGGCGATC 19 87231868 XHMGCoAred_FP6 GACGATCCTTTCTTATTGGCGGCCC 25 87231868 Xhsp70.1 ATTGG 5 88065503 Xhsp70.6 ATTGG 5 88065503 Xhsp70.3 CCAAT 5 87172780 XCCAAT-bf-h CCAAT 5 87257843 Xheat-indf- CTGGAATATTCCCG 14 87257843 XHSTF-hsp70.9 GACCTTATAAGGGC 14 87172780 XHSTF-hsp70.10 GACCGTCGGAGTAG 14 87175642 XCTF/CBP-hs GATTGG 6 87172780 Xhsp70.4 AGAAGGGAAA 10 87175642 Xhsp70 GAAGGGAAAA 10 88065503 Xhsp70.5 GATTGG 6 88065503 XSp1-hsp70 GGCGGG 6 88065503 Xhsp70.2 GGCGGG 6 87175642 XTFIID/TBF?-RS TATAAA 6 87175642 XHAP-hsp83 GAAGTCTCTAGAAGTTTCTAGAGAC 25 84191545 XIE1-I CCCGCCTGGCTGACCGCCCAACGAC 25 87231877 XIE1.1 TTGGCAGTACATC 13 87231877 XNFI-IE1.5 TTGGCTATATGCCAA 15 86274639 Xalpha-4_RS1 GGGGAATCGTCACTGCCGCCCCTTT 25 86259665 Xalpha-4_RS2.1 CGGATGGGCGGGGCCGGGGGTTCGA 25 86259665 XSp1-IE-3.2 GGGCGG 6 85296380 XSp1-IE-3.3 CCCGCC 6 85296380 XSp1-IE-3.4 CCGCCC 6 85296380 XSp1-IE-3.5 CCGCCC 6 85296380 XSp1-IE-4/5 CCCGCC 6 85296380 XSp1-IE-4/5 CCGCCC 6 85296380 XGCN4-ILV1.1 GAGTCA 6 87041486 XGCN4-ILV1.2 TGAGTG 6 87041486 XGCN4-ILV1.3 AAGTCA 6 87041486 XGCN4-ILV2 TGATTC 6 87041486 XIGNF-A-IgH ATTTGCAT 8 86092241 XIgHC.1 ATTTGCAT 8 87092300 XNF-A1-IgHC ATTTGCAT 8 87039335 XNF-A2-IgHc ATTTGCAT 8 87039335 XIgHC.2 ATTTGCAT 8 87014826 XNFuE1-IgHC AGTCAAGATGGCCGATC 17 86298399 XIgHC.20 AAGATGGC 8 87004545 XIgPE-1-IgH CAGCTGGCAGGAAGCAGGTCATGTG 25 87133485 XNFuE3/GTII GTCATGTGGCAAG 13 86298399 XIgHC.8 CATGTGGC 8 85090419 XIgNF-A-IgH ATGCAAAT 8 86092241 XIgPE-2-IgH CCACCAAACCGAAAGTCCAGG 21 87133485 XIgHC.11 GTGTTTTGCTCA 12 87115775 XIgHC.12 ACCACCTG 8 85090419 XIgHC.13 ATGCAAATAG 10 87115775 XIgHC.14 ATTTGCAT 8 87004545 XIgHC.15 ATTTGCAT 8 87004545 XIgPE-3-IgH CTGGGTAATTTGCATTTCTAAAATA 25 87133485 XIgHC.16 ATTTGCAT 8 86313585 XIgHC.20 ATTGCAT 7 86298399 XIgHC.17 TTTTAGGAAGCAAAAACA 18 87174814 XIgHC.18 ATTTGCGT 8 87174814 XIgHC.19 ATGAAAAT 8 87174814 XNFkB-IgkLC GGGGACTTTCC 11 86298399 XIgNF-A-Igk ATTTGCAT 8 86313585 XNF-A1-IgkL ATTTGCAT 8 87039335 XNF-A2-IgkL ATTTGCAT 8 87039335 XIgkLC-1 GGGGATTTCCAAGAGGCCACCTG 23 87257882 Xinsulin GTGGAAA 7 86161694 Xinsulin.2 TTAATAATCTAATTCCC 17 86161694 XINS_US.1 TTTCTGCAGACTTAGC 16 86161694 XR2-b-IFN.1 TTTTTCCCTATTATATATATCATAA 25 86218074 XR1-b-IFN GAGAAGTGAAAGTGGGAAATTCCTC 25 86218074 XIgPE-2-LPV-wt GAATCAACTGAACGCGGAAGCTGTG 25 87004545 XGR-lysozym.2-1 ACAGACTATAAAATTCCTCTGTGGC 25 85137874 XPR-lysozym.2-1 ACAGACTATAAAATTCCTCTGTGGC 25 85137874 XGAL4-MEL1 TTCGGCCATATGTCTTCCGAA 21 86220139 XSp1-MT-I.1 GAGCTCTGCACTCCGCCCGAAAAGT 25 87149062 XSp1?-MT-I.1 GGGGGCGG 8 88065495 XMT-I.2 TGCACACCG 9 88065495 XSp1?-MT-I.2 TGCACTCCGCCC 12 88065495 XMT-I.3 TGCGTCGG 8 88065495 XMT-I.4 TGCGTCGT 8 88065495 XMT-I.5 CTGAGTGCA 9 88065495 XMT-I.6 TGCGCCCGG 9 88065495 XGR-MT-IIA TGTCCT 6 84168159 XAP2-MT-II.1 GCCGAGGCGTCCCCGAGGCGCAAGT 25 87301729 XAP2-MT-II.2 AGGGAACTGACCGCCCGCGGCCCGT 25 88027009 XAP2-MT-II.3 CCGGGTGTTTCGCCTGGAGCCGCAA 25 88027009 XPRTF-MFa1 TTTCCGATTAGGAAT 15 87301711 XPRTF/MATa1.1 TTTCCTAATTAGTCCTATCAATAGA 25 87301711 XPRTF/MATa1.2 CTTCCTAATTAGGCCATTCAACGAC 25 87301711 XPRTF/MATa1.3 TTTCTTCATTGGTACATTCAATGCC 25 87301711 XAP2-MHCI AGGTCAGGGGTGGGGAAGCCCAGGG 25 88027009 XDQ-beta-US1 ATTTGTAT 8 88040427 XAT GGGGATTCCCC 11 88111518 XMMTV-NF-I_RS AAAACCTTAAATAGGTTTAGAA 22 87102873 XGR-MMTV.01 CCAAGGAGGGGACAGTGG 18 84082063 XGR-MMTV.02 ACTAATAGAACATTA 15 84082063 XGR-MMTV.03 TTTTTGGTTACAAACTGTTCTTAA 24 84221898 XGR/PR-MMTV.1 TGTTCT 6 83297683 XGR/PR-MMTV.2 TGTTCT 6 85137874 XGR/PR-MMTV.3 TGTTCT 6 85137874 XGR/PR-MMTV.4 TGTTCT 6 85137874 XGR/PR-MMTV.5 TGTTCT 6 85137874 XGR-MMTV.04 GATGTGAGACAAGTGGTTTCCTGAC 25 84082063 XGR-MMTV.05 GGATCAAAGGTTCTGATCTGAGCTC 25 84082063 XGR-MMTV.06 TTGGCACAGGCTCTTTTTGTGCTGA 25 84082063 XGR-MMTV.07 GGGTCCTGGAAAGGACGATGTCCTA 25 83297683 XNFI-Mo-MuLV? TGAATATGGGCCA 13 87172777 XLVb-Mo-MuL CAGGATA 7 87172777 XMo-MuLV TGTGGTAT 8 87172777 XLVc-Mo-MuL CCTGC 5 87172777 XNFI-Mo-Mu CGGCTCAGGGCCA 13 87172777 XGR?-Mo-MuL AGAACAGATG 10 87172777 Xc-mos_DS1 TGGTTTG 7 87254206 Xc-mos_DS2 CAACCAC 7 87254206 Xc-mos_DS3 GTTTTAA 7 87254206 XIgPE-1-MSV ATATGGGCCAAACAGGATATCTGTG 25 87004545 XEBP20-MSV ACAGGATATCTGTGGTAAGCAGTT 24 88056262 XAP2-c-myc.1 AAAGGGCCGGTGGGCGGGAGATT 23 88027009 XAP2-c-myc.2 CAGCACAGCTCGGGGGTCCTCAG 23 88027009 XCOUP-ovalb GTCAAAGGTCAAA 13 XUAS-PGK_RS GAAATTACCGTCGCTCGTGATTTGT 25 88015532 Xpolyoma.3 ACTGCCCTCCAGAGGGCAGT 20 86176771 Xpolyoma.2 AGTTGCTAGGCAACT 15 86176771 XT-Ag-Py.1 CTCTCCACCCAGGCC 15 85033939 XEBP20-poly AGTGTGGTTTTGCAAGAGGAAGC 23 88056262 XGT-IIc-Py-wt CAGGCCTAGAATGT 14 88082672 XEF-C-polyo AGTTGCTAGGCAACT 15 87041493 XT-Ag-Py.2 CAACAGCTGTTTTTTTTAGTATTAA 25 85033939 XT-Ag-Py.4 AAAAGAAGAGAGGCATTGTAGAGGC 25 85033939 XT-Ag-Py.5 ACTGGCGCCTTGGAGGCGCTGTGGG 25 85033939 XT-Ag-Py.6 ATTAAGCCCCAACCGCCTCTTCCCG 25 85033939 XEFII-RSV TATGCA 6 87144250 XEFI-RSV AAGCACCGTGCATGCCGATTGGTGG 25 87144250 XPRTF/MATa1.4 TTTCCTAATTAGTGTCACAATGACA 25 87301711 XHBsAG-US ACTGGCCAGCAGC 13 87004566 XT-Ag-SV40.1 TAGGC 5 83138977 XT-Ag-SV40.2 GAGGC 5 83138977 XT-Ag-SV40.3 GGGGC 5 83138977 XLSF-SV40 CCGCCC 6 87317587 XSp1-SV40.2 GGGCGGAG 8 86018849 XSp1-SV40.3 GGGCGGAG 8 85061571 XSp1-SV40.4 GGGCGG 6 85061571 XSp1-SV40.1 GGGGCGGG 8 85061571 XAP1-SV40.1 TTAGTCAG 8 87159552 XSV40.1 TCTCAATTAGT 11 87115775 XAP1-SV40.2 TGACTAA 7 87115798 XSV40.2 TGCATGCTTTGCATACTT 18 87014825 XOBF-SV40.1 TGCTTTGCAT 10 87115775 XSV40.3 TGTGGAAAGTCCCCAGGCTCCCCAG 25 87115775 XSV40.16 TGGAAAG 7 87159552 XAP1-SV40.3 TTAGTCAG 8 87159552 XSV40.7 TGACTAATTGA 11 87115775 XOBF-SV40.2 TGTTTGCAT 9 87115775 XSV40.8 TGCATGCTTTGCATACTT 18 87174814 Xoct-B1A-SV CTTTGCAT 8 88082673 Xoct-B1B-SV CTTTGCAT 8 88082673 Xoct-B2-SV4 CTTGCAT 7 88082673 Xoct-B3-SV4 CTTTGCAT 8 88082673 XSV40.9 TGTGGAAAGTCCCCAGGCTCCCCAG 25 87115775 XSV40.12 ACTTTCCACACC 12 88056262 XEBP20-SV40 GGGACTTTCCACACCCTAAC 20 87014825 XSV40.13 TGGAAAG 7 87159552 XAP3-SV40.1 ACTTTCCACACC 12 87301729 XAP3-SV40.2 TTTCCACACCCTAACTG 17 87014825 XSV40.14 ACATTCCACAGC 12 87014825 XGT-IIC-SV4 ACATTCCACAG 11 87014825 XSV40.15 ACATTCCACAGC 12 87014825 XGT-IIBa-SV ACAGCTG 7 88082672 XGT-IIBb-SV ACAGCTG 7 88082672 XGT-IIA-SV40 AGCTGGTTCTTTCC 14 88082672 XSp1-tk.1 ACCCCGCCCA 10 85282613 XCTF/NF-I-t AGCCAAT 7 87078403 XSp1-tk.2 GGGGCGGCGC 10 85282613 XCBP-tk CCAAT 5 86133549 XNF-Y*-tk CCAAT 5 87301730 Xtryp-oxy_GRE.1 CCAGGACATCATGAAAGGGAGCAGT 25 87218520 Xtryp-oxy_GRE.2 ATATGCACAGCGAGTTCTAGTGAGT 25 86313585 XSp1?-U2snR.1 GGGCGG 6 87259982 XSp1?-U2snR.2 ACGCCC 6 87259982 XSP1?-U2snR.3 GGGCGG 6 87259982 XOcta-facto ATGCAAAT 8 87259982 XOBF-U2snRN ATGCAAATAG 10 87115775 XU2snRNA.2 GTGCC 5 87115775 XU5snRNA ATTTGCAT 8 88082680 XU5snRNA.2 GGTGCGCGCCGGT 13 88082680 XPR-uterogl.1 TGTTCTCC 8 87231032 XGR-uterogl TGTTCT 6 87231032 XPR-uterogl.2 AGTCCTTT 8 87231032 XGR-uterogl TGTTCT 6 87231032 XPR-uterogl.3 TGTTCACT 8 87231032 XPR-uterogl.4 TAGAACCCGTGCTCTT 16 87231032 XPR-uterogl.5 TGTTCACT 8 87231032 XGR/PR-uter TGTTCACT 8 87102864 XPR-uterogl.6 TGTCCTCT 8 87133483 XPR-uterogl.7 GAGTGGGAACAACTGTTTGGCAGAG 25 87133483 XWAP.5 CCAAGT 6 87174739 XWAP.6 TTTAAA 6 87174739 XCuE1.4 GTCAAGATGGC 11 89168418 XkE2 GGCAGGTGG 9 89168418 XCuE3.4 GTCATGTGG 9 89168418 XCuE5 TGCAGGTGT 9 89168418 XE1A_element_II SGCGWAA 7 86189935 XE1A_element_I AGGAAGTGACAA 12 86189935 XATF_RS TGACGT 6 88217908 XE1A_RS1 GYRGYTTTC 9 83297292 XE1A_RS2 GTAGTY 6 83297292 XNFI-E3 GGCCAA 6 88040461 XAP1-E3.2 AGATGACT 8 88040461 XCREB-E3.2 TGACG 5 88040461 XFSE2 TGACTCA 7 88151051 XADH_US2 CACCTCCC 8 85215511 XAAT_US1 GTTAATAATTTTC 13 88233915 XAAT_US2 GTGGTTTC 8 88040463 XAAT_US3 TGGTTAATATTCACCA 16 88040463 XE2_RS1 ACCNNNNNNGGT 12 88096566 XE2_RS2 ACCKNNNYCGGTGC 14 88096566 Xconalb_US1 GGAAA 5 83143343 Xconalb_US2 GGAAG 5 83143343 XXRE-cyt450.1 CSTSYTSTCACGCWA 15 87230998 XXRE-cyt450.2 GTGGAAG 7 85182625 XXRE-cyt450.3 AGTGTATTCT 10 85182625 XXRE-cyt450.4 CAGAGRAGGWGG 12 85182625 XXRE-cyt450.5 AGTGGG 6 85182625 XCytR_RS1 TTRTKTRAACGAT 13 86176724 XCytR_RS2 TKYRANNNNNWTCRMR 16 86176724 Xc-fos_US1 GATSBCCWWATWWGGV 16 86272105 XGAL4_RS1 CGGASGACWGTCSTCCG 17 85176930 XGAL4_RS2 TGTAANCGNTNCCAC 15 83155655 XCAP.2 TGCATCA 7 83103095 XNEG_RS1 CCGCCC 6 84282711 XEARLY-SEQ1 YYCCGCCC 8 83110644 XSP1_RS1 GGGCGG 6 85061571 XBOXA-SEQ TGCAAAT 7 86176743 XBOXB-SEQ ACCGAAANNTTTATATANTA 20 86176743 XHEAVY-STR-SEQ CANACCCCAAAGAYA 15 84130174 XAA-CONTROL-SEQ CTGACT 6 83161150 XHVRP-1 GGGNGGA 7 80001962 XHVRP-2 GGGNGGAG 8 80090082 XH/Bsite CACCC 5 87040733 XHBCCDE AGTCACTGTGACC 13 87066756 XARCH-US1 TTTAWA 6 88124189 XCRE.0 WHNRHGYBWV 10 80056640 XAA-CSEQ TGANT 5 83161150 XHVRP3 ATAATATACCTTAT 14 80001962 XHVRP4 GCCAA 5 80001962 XHVRP5 AATGA 5 80001962 XHVRP6 TGACGT 6 80001962 XHVRP7 GGGCGGRR 8 80090082 XCRE.4 ACACTTT 7 80056640 XCAP1 AATGTGATCA 10 84196370 XCAP2 AATGTGATTCA 11 85063773 XCAP3 TAAAAAGTGTGACCTAGATCACATT 25 XhistHO CACGAAAA 8 87102888 Xlegumin_US1 TCCATAGCCATGCAWRCTGMAGAAT 25 86176760 XMAT_gene.1 TGAAACA 7 87273499 XMAT_gene.2 TCRTGTNNWNANNTACATCA 20 85188294 XMAJ-SPERM.1 AGATCT 6 88172456 XSUP-DIS.1 GGCGGG 6 85257452 Xthym/synth_rep1 CGCCGCG 7 87146430 Xthyroglob.1 CCCAGTCAAGTGTTC 15 88040446 Xtrans/recep1 TGACNNA 7 88124258 X|-tub_US1 TTCTCTGGG 9 85215466 Xmal_gene.1 TCMTCC 6 85130804 XMAT_gene.3 ATTACCCAAAAAGGAAATT 19 85188294 Xglob.1 GGGGGGGGGGGGGGGGGGCGGGTGG 25 85242087 Xglob.2 ACACACACACACACACACACACAC 24 83116993 Xcopia_prom.seq1 CTNNAANANTNNNG 14 85242110 XHS_prom1 CTGGAATNTTCTAGA 15 83050937 Xcopia_prom.seq2 NTGGAATATNCTRN 14 85242110 XHS_prom2 CGAGAAGTTTCGTG 14 83050937 XHS_prom3 RCMGGCGC 8 83050937 XHIS_gene.1 TGACT 5 85061237 XMHC_HLA_DQ| ATTTGTAT 8 88040427 XMHC_HLA_H.1 GAAGA 5 86106202 XMHC_HLA_H.2 GGAAGTGA 8 86106202 XMHC_HLA_H.3 GGGTGG 6 86106202 Xhist.1 CCAAT 5 86205261 Xhist.H2B.1 CTCATTTGCATAC 13 86205261 Xhist.H1_gene AAACACA 7 86205261 Xhist.H1.2 AAGAAACACAAA 12 85215498 Xhist.H4.1 GTCAGGTCC 9 84169505 Xhist.H4.2 CCTGA 5 84169505 Xhist.H0_gene RNNYCACGA 9 85254922 Xhist.gene.1 GATCC 5 86205261 Xhist.gene.3 TATAA 5 86205261 Xhist.gene.2 CATTC 5 86205261 XICP4_RS ATCGTCNNNNYCGRC 15 86312880 XHSVIE.0 GCGCACATAAAGG 13 84137573 XHSVIE.1 CGTCCCGGTC 10 84137573 XHSVIE.2 GACCGGGACG 10 84137573 XIgH.1 CTCATGA 7 88262558 XIgH.2 ATGCAAATNA 10 84245856 XIg-kappa.1 GGGGACTTTCC 11 86298399 XIg-dc.1 TNATTTGCAT 10 87066760 XIg-kappa.2 ATTTGCAT 8 86259062 XIg-pd TGCASCTGTGNCCAG 15 84245856 XIg-dc.2 TNATTTGCAT 10 84245856 XIns-IEF1 GCCATCTG 8 88247995 XINF.1 AAGTGA 6 87187632 X|-INF.1 AGTTTCTCYTCTC 13 85188301 X|-INF.2 AARKGA 6 85176973 Xlys.1 TGTGGWWW 8 87230997 Xlys.2 ANNNNTGGCWNNNYGYCM 18 84221360 Xlys.3 TTTGGAAA 8 87230997 XMRE.1 CYTTTGCRYYCG 12 85063782 XMRE.2 GCTSTGCACWCY 12 85063782 XMRE.3 ACCCGGTACACTGTGTCCTCCCGCT 25 84168159 XMRE.4 YKCGCCCGGCYC 12 84168159 XMRE.5 TGCGCCCGCYC 11 85063796 Xgln-ALG.1 GCACYAACATGGTGC 15 86218092 Xnif_seq TGTNNNNNNNNNNACA 16 86232553 XNRE TTTTGCA 7 83195090 XHIS-TRANS.1 TGCACCWWWWTGGTGCA 17 85257487 XNFix.1 TTGCA 5 84205659 XNFix.2 CTGGNNNNNNNNTTGCANNNNNNNN 25 84002273 XNFix.3 YTGGCAYGNNNNTTGCWNNNNNNNN 25 85062817 Xnod_rep1 ATCCAAWCAATCAATTTTACCAATC 25 86176774 XSynF.1 GGGGCAAAT 9 85088471 XSyn.1 NGGGCAAAT 9 85237684 Xrib_US.1 AACATCYRTRCA 12 85062814 Xrib_US.2 AGGTCGACCAGATNTCCG 18 86218097 Xrib_US.3 GACTTGC 7 87051772 X5S_RNA_IC1 WWGGGSSGRG 10 86245047 X16S/32S_rRNA.1 TTTATAT 7 87289030 XribL25.1 WRMAYCCRT 9 87316867 XribINTRONS.1 ACCCATACATTT 12 85215509 Xrib_US.1 WCATCTNTA 9 85062814 XrRNA_seq1 AGGTCGACCAGTANTCCG 18 86218097 XU4B_en.1 GCATG 5 88067753 XLEXA.1 NNCTGWTNNNNNNNCAGNN 19 82259356 XLEXA.2 CTGNCAG 7 85014128 XuvrC_SOS.1 CTGNCAG 7 86176730 XHGRE.1 GNNACAANNTGTYCT 15 85140164 XHGRE.2 TGTTCT 6 85126870 XHGRE.3 TGTTCT 6 84205684 XHGRE.4 ATTCCTCTGT 10 84205684 XHGRE.5 TGTTCT 6 85137874 XHGRE.6 ATTCCTCTGT 10 85137874 XHGRE.7 AGTCCT 6 85126870 XSV40.late.1 GGTACCTAACC 11 83129377 XHSV.tk.1 CCGCCC 6 84205648 XTK.1 CCCCGCCC 8 82223802 XTK.2 GGGGCGGCGCGG 12 82223802 XHSV.tk.2 GGGCGG 6 84205648 XURA.1 ATACGCAT 8 86011594 XURA.2 CCGRTATTCTT 11 86011594 Xuteroglob.1 RYYWSGTG 8 87231032 XSindbis.kdi.25 ATTTTGTTTTTAACATTTC 19 86079570 XsatDNA.1 CCTGTCCGAGATGCGTGCTGATATC 25 86205230 XTMV.1 ATAAA 5 86176720 XvitA2.1 GGTCANTGACC 11 88124970 XvitA2.2 GGTCACAGTGACC 13 88124259 Xvit-estr.1 GGWGYKGAAAG 11 84119500 Xvit-estr.2 CAGGTCAGAGTGACCTG 17 88124970 Xvaccinia.1 CTATTC 6 82025592 Xvaccinia.2 CTATTC 6 85215527 Xmitoch.term1 ATTCTTA 7 84061832 Xrib.term.1 YRTCTG 6 82055570 Xrib.term.2 ACGCGT 6 82055570 Xyeast.term.2 TTTTTATA 8 83232895 Xlambda.a1 CGCTCTTA 8 Xlambda.c GGYGTRYG 8 Xnus.a YGCTCTT 7 85134884 XDHFR.1 ATCRAAWTAGRAAKAGCAAT 20 86232546 X28S_rRNA.1 GGTMGACCAGWWSTCC 16 87230995 X28S_rRNA.2 AGGTCGACCAGWWNTCCG 18 87230995 XrRNA.t2/3 GACTTGC 7 87244323 Xyeast.term.3 TATGT 5 82184406 Xrib.term.3 CATCTTCGGGT 11 82055570 Xlambda.d GGTGTGTG 8 XEBV.IR1_US1 AAGGTGGCCTAGCAACGCGA 20 88335597 XE2_RS.1 GAACCACACCCGGTAC 16 89252826 XE2_RS.2 GCACCGGCGGCGGTAG 16 89252826 XE2_RS.3 CGACCTATCCCGGTAA 16 89252826 XE2_RS.4 GGACCGAACACGTTAT 16 89252826 XE2_RS.5 GAACCAGAACTGGTAA 16 89252826 XE2_RS.6 CCACCAGTAATGGTGC 16 89252826 XE2_RS.7 GTACCGCCATCGGTGC 16 89252826 XE2_RS.8 GCACCGATATAGGTTT 16 89252826 XE2_RS.9 GTACCGTTGCCGGTCG 16 89252826 XE2_RS.10 AAACCGTCTTCGGTGC 16 89252826 XE2_RS.11 TCACCGAAACCGGTAA 16 89252826 XE2_RS.12 ACACCATCACCGTTTT 16 89252826 XE2_RS.13 CAAACGATAAAGGTAG 16 89252826 XE2_RS.14 AAAACAGCAGCGGTTC 16 89252826 XE2_RS.15 CCACCCCTCCTGGTAA 16 89252826 XE2_RS.16 AGAACCTAAACGGTGC 16 89252826 XE2_RS.17 GCACCATGGCCGGTGC 16 89252826 XHMGCoAred_FP4 GTTCGTGACGTAGGCCG 17 87231868 XGAL2_US1 TATCGGGGCGGATCACTCCGAAC 23 86220139 XGAL10_US1 GTACGGATTAGAAGCCGCCGAGC 23 86220139 XGAL10_US2 GAGCGGGTGACAGCCCTCCGAAG 23 86220139 XGAL10_US3 CGAAGGAAGACTCTCCTCCGTGC 23 86220139 XGAL1_US1 CCTCGCGCCGCACTGCTCCGAAC 23 86220139 XGAL7_US1 CTTCGGAGCACTGTTGAGCGAAG 23 86220139 XGAL7_US2 GCTCGGACAACTGTTGACCGTGA 23 86220139 XGAL7_US3 CAACTGTTGACCGTGATCCGAAG 23 86220139 XMEL1 ATTCGGCCATATGTCTTCCGAAA 23 86220139 XGAL80_US1 TACCGGCGCACTCTCGCCCGAAC 23 86220139 XGAL4_CS1 SWWCGGRSSACWSTCSTCCGAAC 23 86220139 XGAL4_CS2 SYWCGGASSACWGTSSTCCGWRS 23 86220139 XE2F-myc GCGGGAAAA 9 89252827 XE2f-Ad5-E2a GCGCGAAAA 9 89252827 XE2F-Ad5-E1a.1 GCGCGAAAA 9 89252827 XE2F-Ad5-E1a.2 CCGCGAAAA 9 89252827 XE2F-Ad12-E1a GCGCGAAAA 9 89252827 XE2F_CS.2 SCGSGAAAA 9 89252827 XHSE-hsp70 CTGGAATATTCCCG 14 87175642 XE4F1_CS ACGTMAC 7 87275829 XE4F1-E4.2 TCGTCAC 7 87275829 XE4F1-E4.3 TCGTCAC 7 87275829 XE4F1-E4.4 ACGTCAC 7 87275829 XE4F1-E4.5 ACGTCAC 7 87275829 XE4F1-E1A.1 GCGTAAC 7 87275829 XE4F1-E1a.2 ACGTAAA 7 87275829 XE4F1-E1a.3 ACGTCAG 7 87275829 XE4F1-E2 ACGTCAT 7 87275829 XE4F1-E3 TCGTCAC 7 87275829 XGR-MTV-I GTTACAAACTGTTCT 15 88092545 XGR-HMT-IIaI GGTACACTGTGTCCT 15 88092545 XGR-RUG-I TGTTCACTCTGTTCT 15 88092545 XGR-RUG-II CGGACACGGAGTCCT 15 88092545 XGR-MRib CTGACACGCTGTCCT 15 88092545 XGR-RUG-III TGTCAGTCTTGTTCT 15 88092545 XGR-MTV-IIA GGTATCAAATGTTCT 15 88092545 XGR-DSC7 GATTTGATCTGTTCT 15 88092545 XGR-CLYS-I GACAACTGTAGAACA 15 88092545 XGR-CLYS-II AATTCCTCTGTGGCT 15 88092545 XGR-rTAT-I CGTACAGGATGGTTCT 16 88092545 XGR-rTAT-II GGACTTGTTTGTTCT 15 88092545 XGR-HGH-I GGCACAATGTGTCCT 15 88092545 XGR-CVIT-II GGATCAATGTGTTCT 15 88092545 XGR-rTO-I TGCACAGCGAGTTCT 15 88092545 XGR-rTO-II CTTTCATGATGTCCT 15 88092545 XGR-MSV-I GGGACCATCTGTTCT 15 88092545 XGR-MSV-II TGTTCCATCTGTTCT 15 88092545 XGR-MSV-III CTGTCTCTCTGTTCC 15 88092545 XGR-COV-I TTTTCTGCCTGTTCT 15 88092545 XGR-HMTIIa-II CCTCCCTCCTGTCCT 15 88092545 XGRE_CS1 GGTACANNNTGTYCT 15 88092545 XAdf-1-Adh CNGCCGNCGCCGNCT 15 90117656 XAdf-1-AntpP1 CNGTCGNCGTCGNCG 15 90117656 XDBF-1-ddc TNAACCGGTTTTGCGG 16 90117656 XDBF-1-Ubx CNAACTGGTCCTGCGG 16 90117656 XdFRA-hmtIIA TGACTCA 7 90117656 XdJRA-hmtIIA TGACTCA 7 90117656 XDTF-1_RS1 GCAACATG 8 90117656 XDTF-1_RS2 GCAACACC 8 90117656 XGAGA-Ubx CGAGAGAG 8 90117656 XGAGA-en AGAGAGAG 8 90117656 XHSTF-hsp70 CTNGAANNTTCNAG 14 90117656 Xzeste-Ubx CGAGCG 6 90117656 Xzeste-white TGAGTG 6 90117656 XAbdB-r_RS1 TAATTTGCAT 10 90117656 XAbdB-r_RS2 TCAATTAAAT 10 90117656 XAntp-Ubx TAATAATAATAATAA 15 90117656 Xbicoid-hb TCCTAATCCC 10 90117656 Xengrailed_RS TCAATTAAAT 10 90117656 Xeve-Ubx TCAATTAAAT 10 90117656 Xeve_RS1 TAATAATAATAATAA 15 90117656 Xeve_RS2 TCAGCACCG 9 90117656 Xftz-Ubx TCAATTAAAT 10 90117656 Xftz_RS1 TAATAATAATAATAA 15 90117656 Xpaired_RS1 TCAATTAAAT 10 90117656 XUbx-Ubx TAATAATAATAATAA 15 90117656 Xzen_RS1 TCAATTAAAT 10 90117656 XCCAAT.4 YNNNNNNRRCCAATCANYK 19 88165047 XCAAT.5 YAGYNNNRRCCAATCNNNR 19 88165047 XCAAT.4 YNNNNNNRRCCAATCANYK 19 88165047 XCAAT.6 NTTGGCNNNNNGCCAN 16 88165047 XGRE_CS3 GGTACANNNTGTTCT 15 89119556 XERE AGGTCANNNTGACCT 15 89119556 XEcRE AGGGTTNNNTGCACT 15 89119556 XTRE TCAGGTCATGACCTGA 16 89119556 XGRE(-) ATYACNNNNTGATCW 15 89119556 XnGRE.1 CCTTTTAGAAAGGACAAAACAGAAT 25 89053052 XnGRE.2 GAGTATAACAGGAACTGAAAATCTT 25 89053052 XnGRE.3 TAAAATACTCTTTGATAATACAT 23 89053052 XnGRE.4 GGCAAATGTTACAAGAAAT 19 89053052 XnGRE.5 CCAGATCTCACCATCATTAT 20 89053052 XnGRE.6 CCTAGATGTTCATTTCTGGTCAGTA 25 89053052 XnGRE.7 GGCAAAAGGGAATGCCTGATTAAAT 25 89053052 XPLF_US1 ACAGTATGATTTGTTTTAGTCAGAG 25 89306613 XGR-MMTV.10 CCTCGTTTTAAGAACAGTTTGTAAC 25 86245074 XGR-MMTV.11 AGCTCAGATCAGAACATTTGATACC 25 86245074 XGR-MMTV.12 ATAGGAAAATAGAACACTAAGAGCT 25 86245074 XGR-MMTV.13 AGATTCCAAAAGAACATAGGAAAAT 25 86245074 XGR-MoMSV.1 ATCAAGGTCAGGAACAGAGAGACAG 25 86245074 XGR-MoMSV.2 CTCAGGGCCAAGAACAGATGGAACA 25 86245074 XGR-MoMSV.3 CTCAGGGCCAAGAACAGATGGTCCC 25 86245074 XGR-MuRFV.1 TGTTTTTCTGAGAACATCAGCTCTG 25 86245074 XGR-MuRFV.2 CAGAAAAACAAGAACAAGGAAGTAC 25 86245074 XGR-MuRFV.3 CGCAGGGACCAGAACAGATGGTTCC 25 86245074 XGR-G/A-FLV.1 ATGTCTGTCCAGGACAGCCAACCGG 25 86245074 XGR-G/A-FLV.2 CGGGATACCGAGAACAGGGCTATAG 25 86245074 XGR-G/A-FLV.3 CTTGAGGCCAAGAACAGTTAAACCC 25 86245074 XGR-visna.1 GCACGAGAGAAGAACATCCCATCGC 25 86245074 XGR-visna.2 ACACAACTGGAGGACAATGCCCTAT 25 86245074 XGR-visna.3 GTGGACTGTCAGGACAGAGAACAAT 25 86245074 XGR-visna.4 GTCAGGACAGAGAACAATGCCTACC 25 86245074 XGR-HuEnRV4-1.1 GGAACTGAGAAGGACAACAGGAGAA 25 86245074 XGR-HuEnRV4-1.2 ATCAGCTAACAGAACAAAAAGTTTT 25 86245074 XGR-HuEnRV14-1.1 CTAGCAGAACAGAACAGAAAGTTTC 25 86245074 XGR-MuEnRV14-1.2 GGGGGCTAGCAGAACAGAACAGAAA 25 86245074 XGR-HIV1.1 AATAAAGGAGAGAACACCAGCTTGT 25 86245074 XGR-ARV-2.1 AATGAAGGAGAGAACAACAGCTTGT 25 86245074 XEIIaE-B GTGGCCGCTGGAGATGACGTA 21 87146375 XEIIaE-C GGGCGTGGGAATTTCCTTGCTCATA 25 87146375 XGC2-GH-NCS TGCTGATGGATAATTTAGAAGCTCC 25 87172787 XIE1-III TAATGACGTATGTTCCCATAGTAAC 25 87231877 XIE1-IV CTTTCCATTGACGTCAATGGGTAAC 25 87231877 XIE1-VIII CTTTCCTACTTGGCAGTACATCTAC 25 87231877 XIE1-IX ATGCGGTTTTGGCAGTACATCAATG 25 87231877 XR2-b-IFN.2 AAAGAGAGTTTTAGAAACTACTAAA 25 86218074 XGR-lysozym.2-2 GTTTTTGACAACTGTAGAACAGAGG 25 85137874 XPR-lysozym.2-2 GTTTTTGACAACTGTAGAACAGAGG 25 85137874 XIgPE-1-Py CAAGGTCCCTCCAGAGGGACGTGTG 25 87133485 XIgPE-2-LPVmut1 GAATCAACTGAACGCGGAAGCTGTG 25 87133485 XIgPE-2-LPVmut2 GAATCAACTGAAAGAGTACGCTGTG 25 87133485 XIgPE-2-LPVmut3 GATCAACTGAAAGAGGAAGCGGGGG 25 87133485 XIgPE-2-LPVmut4 ACTGAAAGAGGAAGCTGTGGTTAGA 25 87133485 XIgkLC-2 GGGGATTTCCAAGAGGCCACCTGGC 25 87257882 XT-Ag-SV40-I GCCTAGGCCTCCAAAAAAGCCTC 23 83138977 XT-Ag-SV40-II GAGGCCGAGGCGGCCTCGGCCTC 23 83138977 XT-Ag-SV40-III ATGGGCGGAACTGGGCGGAGTTAGG 25 83138977 END_OF_FILE if test 80388 -ne `wc -c <'tfd.dat'`; then echo shar: \"'tfd.dat'\" unpacked with wrong size! fi # end of 'tfd.dat' fi if test -f 'bird.dat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'bird.dat'\" else echo shar: Extracting \"'bird.dat'\" \(504 characters\) sed "s/^X//" >'bird.dat' <<'END_OF_FILE' XCOUP GTCAAANGTCAAA 13 REF 11 XEFI (1) AAGCANNNTGCATGC 15 REF 11 XEFI (2) GTGGAAG 7 REF 11 XEFII TATGCA 6 REF 11 XESTROG. RECEPT. GCGTGACCGGAGCTGAAAGAACAC 24 REF 11 XGLUC. RECEPT. (1) ATTCCTCTGT 10 REF 11 XGLUC. RECEPT. (2) CACGGGATCAATGTGTTCTT 20 REF 11 XPROGEST. RECEPT. ATTCCTCTGT 9 REF 11 END_OF_FILE if test 504 -ne `wc -c <'bird.dat'`; then echo shar: \"'bird.dat'\" unpacked with wrong size! fi # end of 'bird.dat' fi if test -f 'dros.dat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'dros.dat'\" else echo shar: Extracting \"'dros.dat'\" \(1062 characters\) sed "s/^X//" >'dros.dat' <<'END_OF_FILE' XAdf-1 GCTGCNGCTGCNNNCGTCGNCTCG 24 REF 11 XB factor (1) TATAAAA 7 REF 11 XB factor (2) TATAAGTA 8 REF 11 Xbcd (1) TCTAATCCC 9 REF 22 Xbcd (2) BBTAATCYV 9 REF dsp/22 XHEAT SHOCK (1) CNNGAANNTTCNNG 14 REF 10,44 XHEAT SHOCK (2) CTNGAANNTTCNAG 14 REF 46 XHEAT SHOCK (3) CTNGAANNTTCNRR 14 REF dsp/44 XHOX TYPE I (1) TCAATTAAAT 10 REF 27,22,23,25,28 XHOX TYPE I (2) TCAWTTAAHT 10 REF dsp/27 XHOX TYPE I (3) MYAWTTRRHK 10 REF dsp/28 XHOX TYPE II (1) TCAGCACCG 9 REF 27,25,22 XHOX TYPE II (2) TBAGCVBCG 9 REF dsp/27 XHOX TYPE III (1) TAATAATAA 9 REF 30,22,26,28 XHOX TYPE III (2) TAATAAYAA 9 REF dsp/30 XTRANSL.START-DROS. MAAMATG 7 REF 45 END_OF_FILE if test 1062 -ne `wc -c <'dros.dat'`; then echo shar: \"'dros.dat'\" unpacked with wrong size! fi # end of 'dros.dat' fi if test -f 'format' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'format'\" else echo shar: Extracting \"'format'\" \(21 characters\) sed "s/^X//" >'format' <<'END_OF_FILE' Xclear Xcat format.txt END_OF_FILE if test 21 -ne `wc -c <'format'`; then echo shar: \"'format'\" unpacked with wrong size! fi chmod +x 'format' # end of 'format' fi if test -f 'format.txt' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'format.txt'\" else echo shar: Extracting \"'format.txt'\" \(1776 characters\) sed "s/^X//" >'format.txt' <<'END_OF_FILE' XYOUR SEQUENCE FORMAT: At present, in this primitive first version, SIGNAL SCAN Xwill only except what is called Staden format (ie., as in Roger Staden). Only Xuppercase letters (A,T,C,&G) are allowed. Blank lines are ignored, no comments Xshould be in the file, no spaces are allowed, and lines can only be 80 Xnucleotides long(or shorter). Please look at the sample sequence file XSAMPLE.SEQ for details (should be included with the program files). The file Xmust be ASCII, which means that if you use a word processor (such as WORD (tm), XWORDPERFECT (tm), etc.) that you will have to export the file into an ASCII Xformat. This is because a word processor adds alot more things to a file than Xmost of you realize (like page formatting, type of printer you selected, and Xmany other things) hidden to the user. For you folks familiar to, and have Xaccess to the Univ. of Wisc. Genetics Computer Group programs, you can use their X"TOSTADEN" formatting program to reformat GenBank files. I hope to make future Xversions of this program that will accept other file formats. X Currently the maximum number of base pairs in an input sequence is 5000. XSIGNAL FORMAT: Print out all *.DAT files to view signal format, sequence, and Xreference numbers for each signal. Print out SIGREF.DOC to view references. XMost references are reviews, and source papers can be found from them. Signals Xuse standard IUB code for ambiguous nucleotides. When there is more than one Xconsensus sequence for a signal, they are designated by (#); GLUC. RECEPT. (5). XSee signal.DAT file (ie. MAMMAL.DAT, BIRD.DAT etc.) for references. You may Xenter your own signals from the keyboard, in IUB format. These signals are not Xkept. To enter your own signals choose Keyboard entry in SIGNAL CLASS window. END_OF_FILE if test 1776 -ne `wc -c <'format.txt'`; then echo shar: \"'format.txt'\" unpacked with wrong size! fi # end of 'format.txt' fi if test -f 'interp' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'interp'\" else echo shar: Extracting \"'interp'\" \(21 characters\) sed "s/^X//" >'interp' <<'END_OF_FILE' Xclear Xcat interp.txt END_OF_FILE if test 21 -ne `wc -c <'interp'`; then echo shar: \"'interp'\" unpacked with wrong size! fi chmod +x 'interp' # end of 'interp' fi if test -f 'interp.txt' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'interp.txt'\" else echo shar: Extracting \"'interp.txt'\" \(1539 characters\) sed "s/^X//" >'interp.txt' <<'END_OF_FILE' XINTERPRETING THE RESULTS: X The results are written to a file that you name, and can be printed out Xusing DOS PRINT command once the program has completed. It is necessary to use Xa new file name each time you run the program, or the results will be appended Xto the end of an existing file. X The results show the name of the signal, the published signal sequence, Xand the first base pair of your sequence that includes that signal. If there Xis a comment "REVERSE OPPOSITE STRAND" after the found signal, it indicates Xthat the signal sequence was found on the opposite strand of your input Xsequence, and that the signal sequence is in the reverse orientation, such that Xthe 1st base pair listed is actually the last base pair in the signal, but Xstill the first base pair in you sequence. Let me illustrate, to wit: XSignal: AATGC (signal found on forward strand) X AATGC XYour seq: 5' GGTTTCTGAAAGCATTGCCTAAATGAGATGAATGCAAAATTTGGCGCGCGTTGTCCC 3' Xopp.strand:3' CCAAAGACTTTCGTAACGGATTTACTCTACTTACGTTTTAAACCGCGCGCAACAGGG 5' X CGTAA X (signal found on reverse opposite strand) XThe 1st bp on the original strand of the found signal is A of AATCG. XThe 1st bp on the revers opp. strand is actually the G of GCATT of your Xoriginal sequence, which if you make it the opposite strand, and reverse it is XAATGC. X Are signals on the opposite strand important? At least sometimes, see Ref X5 for the effect of deletions on an inverted CCAAT box. END_OF_FILE if test 1539 -ne `wc -c <'interp.txt'`; then echo shar: \"'interp.txt'\" unpacked with wrong size! fi # end of 'interp.txt' fi if test -f 'mammal.dat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'mammal.dat'\" else echo shar: Extracting \"'mammal.dat'\" \(7281 characters\) sed "s/^X//" >'mammal.dat' <<'END_OF_FILE' XAP-1 (1) ATGAGTCAGA 10 REF 11 XAP-1 (2) TTAGTCAG 8 REF 11 XAP-1 (3) GTGAGTGAG 9 REF 15 XAP-1/PEA1 TKAGTCA 7 REF 7 XAP-2 (1) CCCCAGGC 8 REF 1 XAP-2 (2) CCGCCCGCGG 10 REF 11 XAP-2 (3) CTGGGGANNCTGGGGA 16 REF 11 XAP-2 (4) GAGCCTGGGGACTTT 15 REF 11 XAP-2 (5) TGGGGA 6 REF 11 XAP-2 (6) TGGGGANTCCCCA 13 REF 11 XAP-2 (7) TTGGGGNNCCCCAA 14 REF 11 XAP-3 (1) ACTTTCCACACC 12 REF 11 XAP-3 (2) TTTCCACACCCTAACTG 17 REF 11 XAP-3 (3) GGGTGTGGAAAG 12 REF 7 XAP-4 CAGCTGTGG 9 REF 7 XAP-5 CTGTGGAATG 10 REF 7 Xc-JUN/AP-1 (1) TGACTCA 7 REF 14 Xc-JUN/AP-1 (2) VTGASTMW 8 REF 0 XC/EBP TGTGGAAAG 9 REF 1 XCAC BOX CCCCACCC 8 REF 17 XCACCC BOX CACCC 5 REF 19 XCCAAT BOX GGYCAATCT 9 REF 16 XC/EBP TGTGGWWWG 9 REF 41 XCP1/CEBP/CTF/NF-Y CCAAT 5 REF 1,7,11 XCREB TGACGTCA 8 REF 1 XCREB/ATF KWCGTCA 7 REF 7 XCTF (1) AGAAGGGAAAA 11 REF 11 XCTF (3) CCAATC 6 REF 11 XCTF/NF-1 (1) AGCCAAT 7 REF 11 XCTF/NF-1 (2) GCCAAT 6 REF 1 XCTF/NF-1 (3) TGGCTNNNAGCCAA 14 REF 7 XE2aE-CB TGGGAATT 8 REF 7 XE4TFI GGAAGTG 7 REF 7 XEBP20 (1) GGGACTTTCCACACCCTAAC 20 REF 11 XEBP20 (2) TGTGGWWWG 9 REF 7 XEBP20 (3) AGTGTGGTTTTGCAAGAGGAAGC 23 REF 11 XEF2 TTTCGCGC 8 REF 7 XEF-C AGTTGCNNNGCAACT 15 REF 11 XENKCRE-1 TGGCGTA 7 REF 18 XENKCRE-2 TGCGTCA 7 REF 18 Xf-EBP GATGTCCNNNNNNGGACATC 20 REF 11 XGLUC. RECEPT.(1) AGAACAT 7 REF 11 XGLUC. RECEPT.(2) AGATCAGTAGATCAGA 16 REF 11 XGLUC. RECEPT.(3) AGTGTTCT 8 REF 11 XGLUC. RECEPT.(4) KGTACANNNTGTTCT 15 REF 1 XGLUC. RECEPT.(5) GNNACAANNTGTCCT 15 REF 11 XGLUC. RECEPT.(6) TAGAACANNNAAGTCC 16 REF 11 XGLUC. RECEPT.(7) TGTTCACT 8 REF 11 XGLUC. RECEPT.(8) WSTGWTCT 8 REF 12 XGT-IIA AGCTGGTTCTTTCC 14 REF 11 XGT-IIBa (1) ACAGCTG 7 REF 11 XGT-IIBa (2) GTCATGTGGCAAG 13 REF 11 XGT-IIBb ACAGCTG 7 REF 11 XGT-IIC ACATTCCACAG 11 REF 11 XH4TF-1 GATTTC 6 REF 11 XHEAT SHOCK (1) CTNGAANNTTCNAG 14 REF 12 XHEAT SHOCK (2) GACCTTATAAGGGC 14 REF 4 XHEAT SHOCK (3) GACCGTCGGAGTAG 14 REF 11 XHEAT SHOCK (4) GACCTTATAAGGGC 14 REF 11 Xheat-ind.f. CNNGAANNTTCNNG 14 REF 11 XHeLa B factor TGGGGANTCCCCA 13 REF 11 XHiNF-A AGAAATG 7 REF 11 XHOX 1.3 BINDING CATTAGTG 8 REF 6 XIgNF-A ATGCAAAT 8 REF 11 XIgNF-A1 ATTTGCAT 8 REF 11 XIgNF-A2 ATTTGCAT 8 REF 11 XIgPE-1 (1) CAGGTGGC 8 REF 11 XIgPE-1 (2) TGTGGAAA 8 REF 11 XIgPE-2 CCACCAAACCGAAAGTCCAGG 21 REF 11 XIRF-1 AAGTGA 6 REF 42 XKBF1 GGGGATTCCCCAT 13 REF 11 XMLTF/USF GGCCACGTGACC 12 REF 7 XNF-1 (1) TCGNNNNNGCCAA 13 REF 11 XNF-1 (2) TGGCNNNNNGCCAAC 15 REF 11 XNF-1 (3) TTGGAATCTATCCAA 15 REF 11 XNF-1 (4) TTTTTGGCAAGGAT 14 REF 11 XNF-kB GGGGACTTTCC 11 REF 11 XNF-E1 MYWATCWY 8 REF 17 XNF-E2/AP1 TGACTCA 7 REF 17 XNF-uE1 AGTCAAGATGGCCGATC 17 REF 11 XNF-uE3 GTCATGTGGCAAG 13 REF 11 XOCT-1 & OCT-2 ATTTGCAT 8 REF 1 Xoct-B1A/B1B/B2/B3 CTTTGCAT 8 REF 11 Xoct.-bind.f. (1) ATGCAAATAG 10 REF 11 Xoct.-bind.f. (2) TGCTTTGCAT 10 REF 11 Xoct.-bind.f. (3) TGTTTGCAT 9 REF 11 XPEA1 TGACTAANTGA 11 REF 11 XPEA2 (1) ACTAACTGACCGCAGCTGGCC 17 REF 11 XPEA2 (2) ACTGACCGC 9 REF 11 XPEA2 (3) GACCGCA 7 REF 7 XPEB1 GACATCCTCTTTTAATTAGTTG 18 REF 11 XPOLY A+ AATAAA 6 REF 0 XPRE/GRE GTTACAAACTGTTCT 15 REF 18 XPROGEST RECEPT (1) TGTCCTCT 8 REF 11 XPROGEST RECEPT (2) TGTTCACT 8 REF 11 XPROGEST RECEPT (3) TGTTCCCA 8 REF 11 XPROGEST RECEPT (4) TGTTCT 6 REF 11 XRNA DEGRADATION ATTTA 5 REF 21 XSCM-ind.f. CAGTTCCCGTCAATC 15 REF 11 XSRF (1) GATGTCCNNNNNNGGACATC 20 REF 11 XSRF (2) CCTTTTATGG 10 REF 15 XSRF (3) CCTTATATGG 10 REF 15 XSRF (4) CCTTTTCC 8 REF 5 XSRF (5) GATGTCCATATTAGGACATC 20 REF 1 XSRF (6) CCWWWWWWGG 10 REF 43 XSp1 GGGCGG 6 REF 1 XT3 RECEPTOR AGGTAAGNNNAGGGGACG 18 REF 11 XTATA BOX (1) TATAAA 6 REF 10 XTATA BOX (2) TATAWAW 7 REF 16 XTATA BOX (3) TATAA 5 REF 7 XTHY REC ELEM CAGGGACGTGACCGCA 16 REF 8 XTHY REC ELEM:SYN TCAGGTCATGACCTGA 16 REF 8 XTRAN.START-KOZAK ACCATGG 7 REF 2 XTRAN.START-CONSEN. RNNATGR 7 REF 2 Xv-MYB YAACKG 6 REF 9 XX-box bind.prot. CCTAGCAACAGATG 14 REF 11 END_OF_FILE if test 7281 -ne `wc -c <'mammal.dat'`; then echo shar: \"'mammal.dat'\" unpacked with wrong size! fi # end of 'mammal.dat' fi if test -f 'program' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'program'\" else echo shar: Extracting \"'program'\" \(22 characters\) sed "s/^X//" >'program' <<'END_OF_FILE' Xclear Xcat program.txt END_OF_FILE if test 22 -ne `wc -c <'program'`; then echo shar: \"'program'\" unpacked with wrong size! fi chmod +x 'program' # end of 'program' fi if test -f 'program.txt' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'program.txt'\" else echo shar: Extracting \"'program.txt'\" \(1664 characters\) sed "s/^X//" >'program.txt' <<'END_OF_FILE' X SIGNAL SCAN is offered to as is, and so are its results, with no Xpromises. A signal, defined here, is any short DNA sequence that that may have Xknown significance. What SIGNAL SCAN will do is find homologies of published Xsignal sequences in your sequence, most of these transcriptional elements. It Xcannot, at this time, predict if what it does find, has any meaning. The Xinterpretation of those results are up to you. Most signal elements found Xwill probably not have any meaning, as the elements are in the wrong milieu, Xwrong cell type, or wrong organism. As a consequence, there will be many Xmore erroneous signals found than significant ones. X The significance varies greatly with the signal. There are many matches Xfor CP1 in any sequence because it is a very short sequence with a high Xprobability of random occurrence. There are much fewer, and more likely Xsignificant glucocorticoid elements because of the much larger signal sequence. X There is also a great possibility that signals that are in your sequence Xwill be missed by SIGNAL SCAN, even if those signals are in the SIGNAL.DAT Xfiles. This can happen if your signal does not fall within the consensus of Xthe reported signal. The accuracy of the consensus signal varies greatly Xbetween different signals. I urge you to review the references, included with Xthis program, before you take any results seriously. Most of the references Xare reviews of signals and not the main source papers, but you can get at the Xsource papers from the reviews. X As SIGNAL SCAN, and the field of Molecular Genetics evolves, the Xpredictive value of this program should increase in future releases. END_OF_FILE if test 1664 -ne `wc -c <'program.txt'`; then echo shar: \"'program.txt'\" unpacked with wrong size! fi # end of 'program.txt' fi if test -f 'running' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'running'\" else echo shar: Extracting \"'running'\" \(22 characters\) sed "s/^X//" >'running' <<'END_OF_FILE' Xclear Xcat running.txt END_OF_FILE if test 22 -ne `wc -c <'running'`; then echo shar: \"'running'\" unpacked with wrong size! fi chmod +x 'running' # end of 'running' fi if test -f 'running.txt' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'running.txt'\" else echo shar: Extracting \"'running.txt'\" \(1466 characters\) sed "s/^X//" >'running.txt' <<'END_OF_FILE' XGROUP SIGNAL SCAN, LINEAR SCAN BY SEQUENCE, or MAP? X Group Signal Scan groups the results of the search by signal, so that all Xof the signal groups are together. Linear scan lists the different signals Xpresent in your sequence as it moves slowly along your sequence. Map shows Xyour sequence and displays signals below it. The choice of output produces the Xsame result, the preference is up to you. X XWHAT NEXT? X You are prompted for the file name the contains your sequence, which must Xbe in Staden format, see SAMPLE.SEQ file for example, and HELP FORMAT. Next Xyou are prompted for the class of signals you want to search your sequence Xwith; this selects which signal data file SIGNAL SCAN will use in the search. XYou can choose Keyboard entry to enter your own signals. You are then prompted Xfor a filename that you wish to store the search results in, which can be any Xlegal DOS file name, such as "SAMPLE.SIG". You must use a new file name for Xeach new search, otherwise the results will be appended to the older file. As Xthe program runs, the results are saved in this file, and you can print it out, Xdelete it, or give it to a friend. X XHOW LONG DOES THIS SUCKER TAKE TO WORK ANYWAY? X Oh, about 7.5' for 3000bps, on a computer with a Norton SI of 4, using XMammmal signals in a signal group search. Less on less and more on more. I Xhope to increase its speed later. Right now its running slower with each Xsignal I add, but at least it's running. END_OF_FILE if test 1466 -ne `wc -c <'running.txt'`; then echo shar: \"'running.txt'\" unpacked with wrong size! fi # end of 'running.txt' fi if test -f 'sample.seq' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'sample.seq'\" else echo shar: Extracting \"'sample.seq'\" \(2605 characters\) sed "s/^X//" >'sample.seq' <<'END_OF_FILE' XAGATCTTCCAGGCTGGATAAATAAACAAATCAGATAGCAAACTAATGGCA XCGAAAAACATATTTTCACGGAGGAAAAAAATGATTCTGGTTATACGAGTG XTATGGAATTTGACCTCGCCTCGGAGAAACACTACACAAAAGCTGTCTTTA XATAGACGCCTGTGGTTTAAGAGCGGCAGGGGCACTGTCCTTCATGCGTTC XACAAAAACAGAGCCGTAATTGTGGCTGCTGCTGTGGGCAGGATTTATTTC XTTCAATTGGCTAAATCGTCTTCCCTTCCTCGAAGGTGATATCTGTGTTTT XCAAAATTCACAGCTGCCGGCCGGGGGCTGGCAAACCGACCCCAACCTCTA XCACAAAAATAAGAGGGGATACAAAGCCGGGGAAATAAAGTTGTTGTAAAT XAATTCTAAGTCACCACCTCCCCCGAATCCTCTGTATCCTCGCCGGGCGTG XCGATCGGCAGCTGACGGCCTCACAATTGGTACGTCCTAATGGAACTGCGA XGGGAAATGCAATAATTTTGCCATAATGGGCTGTAACCTCAATTCGACCCC XGGCCCTTGAAGCCCGAGGTCGGAAGCGAAGCGATGCGCCCAGTCTCCAGC XGGGTGGCGCTCGAGTCCGACTGAACGGCGGCAACGGGTGGCGGGGACGCG XCCCAGGGCGCGCGCGCCACCCCTCTTGCCTCCACCCAACTCCCCCATTAG XTGCACGAGTTTACCTCTAGAGGTCATCAGGCAGGATTTACGACTGGACAA XCAAAAGCACGTGATTCGAAGTCGTACCCCATATTTGGGTGCCTACGTAGG XAGGGAACCGAGTACATGTCCCAGTCATTTCCATAATTCATCATAAATTGT XGCAAGGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACA XCATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCG XCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTT XCCGTGAGCGAACAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTAC XGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGTTCGGGTTCCGG XCCACTTTGGCTCCGGCGAGCGCGCCCGCAGCTACGCGGCTGGGGCCAGTG XCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCG XCCACCGCCCGACCCGCTGCCCTGCTCAGCGGTGGCCCCCTCGCCCGGCAG XCGACAGCCACCACGGCGGGAAAAACTCCCTGGGCAACTCCAGCGGCGCCT XCGGCCAACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACG XGCGTCCGCAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGGGCGC XCCAGAGCGAGCCGAGCCCGGCGCCGCCCGCTCAGCCCCAGATCTACCCCT XGGATGCGCAAGCTGCACATTAGTCACGACAATATAGGTGGCCCAGAAGGC XAAAAGGGCCCGGACGGCCTACACTCGCTACCAGACCCTGGAGCTGGAGAA XAGAATTCCACTTCAACCGCTACCTGACCCGCCGAAGAAGGATCGAAATAG XCTCATGCCCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAAC XAGGAGGATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGTATGGC XCGCGGCAGGGGGGGCTTTCCGCCCCTGAGCATCTGAGCGGCCAAAGTACT XGAGCAGTAGTAGCCGGGCAGCTCTCTGTAGTGTCAGTACTAAGGTGACTT XTCTGAAACTCCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGC XCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTG XTATAAGTAGATCTGCTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCT XTGAAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTA XCTTGAAGTAACTAAAACAAAAAAAAAAAAAAAAGAAAAGAGAAAAAAAAA XCTACTCACACAAAAAGCCCCCCCACCTCTTTAGTGCCAATGTTGTGTGTT XGCACTTGAGTTCTTTAATGTGCATGTACGTGGAAGTGTTCCTGTCTCAAT XAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT XGTAATTAATGCTGTTGTAGAGGTGACTTGATAAGACACAAATTAACTTGT XTCAACGTGTAGTGGCTAGTGGCTCTGTGACGAAAACTGTGACTCCAAGCG XGTGTGTCCCTGCGTGCCTTTGTAGGACCCTTTGCACGAACTCTGGAAGTG XGCTCTTATAAGCGCAGTTCAGTGATGTATGTTTTTGTGAAAAAGTTACAA XATATTGTCCAAGTCTGGCTGTTTAAGCAAACTGTGATCAGCTTTTTTTTT XTTTTTGTATTTGTTTTTAAGGAAAAAAAACACTGACTGGAAACAAAACAA XAATAAACTTTCTATTGTAAGTTCTCTTGGTCTGATTTATGCCAAATAGCA XAGC END_OF_FILE if test 2605 -ne `wc -c <'sample.seq'`; then echo shar: \"'sample.seq'\" unpacked with wrong size! fi # end of 'sample.seq' fi if test -f 'scanl.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'scanl.c'\" else echo shar: Extracting \"'scanl.c'\" \(11694 characters\) sed "s/^X//" >'scanl.c' <<'END_OF_FILE' X/* SCANL.C */ X X X#include X#include X#include X#include "ansi.h" X X#define USER "USERSIG" X#define MAXSIG 2000 /* Max. number of signals read from file */ X#define NAMELEN 21 /* Name of signal, length */ X#define SEQLEN 26 /* Length of signal sequence, MUST be 1 greater X than length in SIGNAL.DAT. Note that if X change this length, also change testsignal X length.*/ X#define TEMPLEN 81 /* Length of line read for input seq. file, X also used in reading signal length integer*/ X#define SEQUENCE 100000 /* Maximum sequence length, may reset later X if so, also change FILELEN */ X#define FILELEN 1250 /* Maximum number of lines to be read from an X input seq. file, 70 lines = 5600bps*/ X X#define clrscr() printf("%c%c%c%c", 27, 91, 50, 74) X Xint getsignals(); /* Input signals function*/ Xvoid getseqfilename(); /* To get name of input seq. file*/ Xvoid getseq(); /* Get sequence.*/ Xvoid savename(); Xvoid sigclass(); Xvoid display(); /* used to display signal class choices */ Xint compare(); Xvoid pause(); X X/* Global structure declarations: */ X Xstruct sigstruct /* The signal-information structure. */ X { X char signame[NAMELEN]; X char sigseq[SEQLEN]; X int siglen; X X } sigarray[MAXSIG]; /* The array of all signals in file. */ X X Xchar seq[FILELEN][TEMPLEN]; /* The array of sequence lines read from an X ASCII text file, each line in seq. file is X a 1D array of characters TEMPLEN long (80) X and FILELEN long (100) lines in the 2D, this X allows about 8000 nucleotides, except seq X limit is now only 5000 */ Xchar SEQFILE[13]; /* The array for the input seq. file name*/ Xchar SAVEFILE[13]; /* Array for results save file name */ Xchar SIGNALX[13]; /* Array for signal data file name*/ Xchar sequence[SEQUENCE]; /* Array to store the concat. final sequence. */ X Xchar window[SEQUENCE]; /* Array for the test window for sequence.*/ XFILE *sigwrite; /* Opens file to write results of search */ XFILE *seqread; Xint seqcount; X Xmain() X { X register int i, j, m, p, q; X int result, sigcount, basepairs; X X X char testsignal[25]; X char opprevsig[25]; X X clrscr(); X getseqfilename(); X clrscr(); X savename(); X clrscr(); X sigclass(); X X X for (m = 0; m < seqcount; m++) /* Used to strip \n's from seq X lines in text file*/ X seq[m][strlen(seq[m]) - 1] = '\0'; X X for (m = 0; m < seqcount; m++) /* Concat's seq. lines from seq X file into same array line*/ X strcat(sequence, seq[m]); X X clrscr(); X basepairs = strlen(sequence); X printf("%s: %4d base pairs", SEQFILE, basepairs); X printf(" Signal database file: %s\n\n", SIGNALX); X printf("SIGNAL NAME SIGNAL SEQ. SEARCH SEQ., 1ST bp of signal\n"); X printf("____________________________________________________________________________\n\n"); X X /* Open the save file in append mode. */ X X sigwrite = fopen(SAVEFILE, "at"); X X /* Write the name of the signal to a file */ X X fprintf(sigwrite, "%s: %4d base pairs", SEQFILE, basepairs); X fprintf(sigwrite, " Signal database file: %s\n\n", SIGNALX); X fprintf(sigwrite, "SIGNAL NAME SIGNAL SEQ. SEARCH SEQ., 1ST bp of signal\n"); X fprintf(sigwrite, "____________________________________________________________________________\n"); X X fclose(sigwrite); X X X sigcount = getsignals(); X X i = 0; /* Reset i to zero for next comparison. */ X do /* Compare to search sequence. */ X { X X for (j = 0; j < sigcount; j++) /* For each signal sequence:*/ X { X X strcpy(testsignal, sigarray[j].sigseq); /* Make working copy of signal seq*/ X testsignal[sigarray[j].siglen] = '\0'; X X result = compare(&sequence[i], testsignal); X if (result == 0) X { X printf("%s: %-25s: %4d\n", sigarray[j].signame, X sigarray[j].sigseq, i + 1); X /* Open the save file in append mode. */ X X sigwrite = fopen(SAVEFILE, "at"); X X /* Write the name of the signal to a file */ X fprintf(sigwrite, "%s: %-25s: %4d%\n", X sigarray[j].signame,sigarray[j].sigseq, i + 1); X X fclose(sigwrite); X X } X X strcpy(opprevsig, testsignal); X for (p = strlen(testsignal) - 1, q = 0; q < strlen(testsignal); p--, q++) X { X if (testsignal[p] == 'A') X opprevsig[q] = 'T'; X X else if (testsignal[p] == 'T') X opprevsig[q] = 'A'; X X else if (testsignal[p] == 'C') X opprevsig[q] = 'G'; X X else if (testsignal[p] == 'G') X opprevsig[q] = 'C'; X X else if (testsignal[p] == 'R') X opprevsig[q] = 'Y'; X X else if (testsignal[p] == 'Y') X opprevsig[q] = 'R'; X X else if (testsignal[p] == 'M') X opprevsig[q] = 'K'; X X else if (testsignal[p] == 'K') X opprevsig[q] = 'M'; X X X else if (testsignal[p] == 'D') X opprevsig[q] = 'H'; X X else if (testsignal[p] == 'H') X opprevsig[q] = 'D'; X X else if (testsignal[p] == 'B') X opprevsig[q] = 'V'; X X else if (testsignal[p] == 'V') X opprevsig[q] = 'B'; X X } X X X result = compare(&sequence[i], opprevsig); X if (result == 0) X { X printf("%s: %-25s: %4d Reverse opposite strand\n", sigarray[j].signame, X sigarray[j].sigseq, i + 1); X X /* Open the save file in append mode. */ X X sigwrite = fopen(SAVEFILE, "at"); X X /* Write the name of the signal to a file */ X fprintf(sigwrite, "%s: %-25s: %4d Reverse opposite strand\n", X sigarray[j].signame,sigarray[j].sigseq, i + 1); X X fclose(sigwrite); X X X } X X X } X } X while (sequence[i++] != '\0'); X printf("END OF SEARCH! "); X printf("\nRESULTS OF SEARCH SENT TO FILE: %s\n", SAVEFILE); X X X } /* END OF MAIN */ X Xint getsignals() X { X FILE *sigread; X int sigcount = 0; /* counts the number of signals in the file*/ X char strlen[TEMPLEN]; /* templen holds siglen for atoi conversion */ X X sigread = fopen(SIGNALX, "rt"); X X X X /* if file exists, read its contents. */ X X if (sigread != NULL) X { X /* Stop reading at MAXSIG or end of file. */ X X while ((sigcount < MAXSIG) && X (fgets(sigarray[sigcount].signame, NAMELEN, X sigread) != NULL)) X { X X /* Read the signal sequence. */ X X fgets(sigarray[sigcount].sigseq, SEQLEN, sigread); X X X /* Read the signal length as a string value, and X then use atoi to convery the string to a int val*/ X X fgets(strlen, TEMPLEN, sigread); X sigarray[sigcount++].siglen = atoi(strlen); X X } X fclose(sigread); X } X return(sigcount); X } Xvoid getseq() X { X int z; X seqcount = 0; X seqread = fopen(SEQFILE, "rt"); X if (seqread != NULL) X { X while ((seqcount < FILELEN) && X (fgets(seq[seqcount], TEMPLEN, seqread) != NULL)) X { X if(isupper(seq[seqcount][0]) == 0) X { X for(z = 0; z < strlen(seq[seqcount]); z++) X { X seq[seqcount][z] = toupper(seq[seqcount][z]); X } X } X seqcount++; X } X fclose(seqread); X seqcount = seqcount; X X } X else /*if no seqfile is found*/ X { X printf("FILE NOT FOUND"); X printf("Make sure file is in current directory"); X printf("Make sure you included the file extension"); X pause(); X clrscr(); X getseqfilename(); X } X } X X X X X Xint compare(window, testsignal) Xchar window[]; Xchar testsignal[]; X{ X int i, result = 0; X X for (i = 0; i < strlen(testsignal); i++) X { X if (result == 1) X break; X X X X if (testsignal[i] == window[i] ) X result += 0; X X else if (testsignal[i] == 'N' && window[i] == 'A' || X testsignal[i] == 'N' && window[i] == 'T' || X testsignal[i] == 'N' && window[i] == 'C' || X testsignal[i] == 'N' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'R' && window[i] == 'A' || X testsignal[i] == 'R' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'Y' && window[i] == 'C' || X testsignal[i] == 'Y' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'M' && window[i] == 'A' || X testsignal[i] == 'M' && window[i] == 'C') X result += 0; X X else if (testsignal[i] == 'W' && window[i] == 'A' || X testsignal[i] == 'W' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'S' && window[i] == 'C' || X testsignal[i] == 'S' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'K' && window[i] == 'G' || X testsignal[i] == 'K' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'D' && window[i] == 'A' || X testsignal[i] == 'D' && window[i] == 'G' || X testsignal[i] == 'D' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'H' && window[i] == 'A' || X testsignal[i] == 'H' && window[i] == 'C' || X testsignal[i] == 'H' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'V' && window[i] == 'A' || X testsignal[i] == 'V' && window[i] == 'C' || X testsignal[i] == 'V' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'B' && window[i] == 'C' || X testsignal[i] == 'B' && window[i] == 'G' || X testsignal[i] == 'B' && window[i] == 'T') X result += 0; X X X else result = 1; X } /* end of if */ X return(result); X X} /* end of compare */ X X X Xvoid sigclass() X{ X char response; X display(); X X /*Get the user's choice, convert it to X uppercase, and display it on the screen. */ X response = getchar(); X response = toupper(response); X X /* select the signalx.dat file */ X X switch(response) X { X case 'M' : X strcpy(SIGNALX, "mammal.dat"); X break; X X case 'B' : X strcpy(SIGNALX, "bird.dat"); X break; X X case 'X' : X strcpy(SIGNALX, "xenopus.dat"); X break; X X case 'D' : X strcpy(SIGNALX, "dros.dat"); X break; X X case 'Y' : X strcpy(SIGNALX, "yeast.dat"); X break; X X case 'G' : X strcpy(SIGNALX, "tfd.dat"); X break; X X case 'K' : X strcpy(SIGNALX, "user.dat"); X system(USER); X pause; X break; X X } X} /*end of sigclass()*/ X Xvoid getseqfilename() X { X CUR_MOVE(11,25); X X printf("\033[1m"); X printf("Sequence file name? "); X printf("\033[0m"); X printf("\033[1m"); X gets(SEQFILE); X printf("\033[0m"); X getseq(); X } X Xvoid savename() X { X CUR_MOVE(11, 25); X printf("\033[1m"); X printf("File name to SAVE results? "); X printf("\033[0m"); X printf("\033[1m"); X gets(SAVEFILE); X printf("\033[0m"); X X } X X X/* The display function displays the menu on the screen. */ Xvoid display() X { X printf("\033[7m"); X CUR_MOVE(6, 25); X printf("SELECT SIGNAL CLASS"); X printf("\033[0m"); X printf("\n"); X printf("\033[1m"); X printf("\n\n\t\t\tM"); X printf("\033[0m"); X printf("ammal"); X printf("\033[1m"); X printf("\n\n\t\t\tB"); X printf("\033[0m"); X printf("ird"); X printf("\033[1m"); X printf("\n\n\t\t\tA"); X printf("\033[0m"); X printf("mphibian"); X printf("\033[1m"); X printf("\n\n\t\t\tI"); X printf("\033[0m"); X printf("nsect"); X printf("\033[1m"); X printf("\n\n\t\t\tY"); X printf("\033[0m"); X printf("east"); X printf("\033[1m"); X printf("\n\n\t\t\tG"); X printf("\033[0m"); X printf("hosh TFD"); X printf("\033[1m"); X printf("\n\n\t\t\tK"); X printf("\033[0m"); X printf("eyboard entry\n\n"); X printf("CHOICE = "); X X X } /* end of display */ X X X/* The pause function creates a pause in the action so the X user can examine the output screen. */ X Xvoid pause() X { X printf("\033[7m"); X printf("Press a key..."); X printf("\033[0m"); X getchar(); X X } /* end of pause */ X X X/* END */ END_OF_FILE if test 11694 -ne `wc -c <'scanl.c'`; then echo shar: \"'scanl.c'\" unpacked with wrong size! fi # end of 'scanl.c' fi if test -f 'scanm.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'scanm.c'\" else echo shar: Extracting \"'scanm.c'\" \(12273 characters\) sed "s/^X//" >'scanm.c' <<'END_OF_FILE' X/* SCANM3.C fixes bug that didn't allow map file to be printed. */ X X#include X#include X#include X#include "ansi.h" X X X#define USER "USERSIG" /* TO start prog. to enter user signal */ X X#define MAXSIG 2000 /* Max. number of signals read from file */ X#define NAMELEN 21 /* Name of signal, length */ X#define SEQLEN 26 /* Length of signal sequence, MUST be 1 greater X than length in SIGNAL.DAT. Note that if X change this length, also change testsignal X length.*/ X#define TEMPLEN 81 /* Length of line read for input seq. file, X also used in reading signal length integer*/ X#define SEQUENCE 100000 /* Maximum sequence length, may reset later X if so, also change FILELEN */ X#define FILELEN 1250 /* Maximum number of lines to be read from an X input seq. file, 70 lines = 5600bps*/ X X#define clrscr() printf("%c%c%c%c", 27, 91, 50, 74) X Xint getsignals(); /* Input signals function*/ Xvoid getseqfilename(); /* To get name of input seq. file*/ Xvoid getseq(); /* Get sequence.*/ Xvoid savename(); Xvoid sigclass(); Xvoid display(); /* used to display signal class choices */ Xint compare(); Xvoid pause(); X X/* Global structure declarations: */ X Xstruct sigstruct /* The signal-information structure. */ X { X char signame[NAMELEN]; X char sigseq[SEQLEN]; X int siglen; X X } sigarray[MAXSIG]; /* The array of all signals in file. */ X X Xchar seq[FILELEN][TEMPLEN]; /* The array of sequence lines read from an X ASCII text file, each line in seq. file is X a 1D array of characters TEMPLEN long (80) X and FILELEN long (100) lines in the 2D, this X allows about 8000 nucleotides, except seq X limit is now only 5000 */ Xchar SEQFILE[13]; /* The array for the input seq. file name*/ Xchar SAVEFILE[13]; /* Array for results save file name */ Xchar SIGNALX[13]; /* Array for signal data file name*/ Xchar sequence[SEQUENCE]; /* Array to store the concat. final sequence. */ X Xchar map[SEQUENCE]; /* Array for the test window for sequence.*/ XFILE *sigwrite; /* Opens file to write results of search */ XFILE *seqread; Xint seqcount; X Xmain() X { X register int i, j, k, m, p, q; X int result, sigcount, basepairs; X X char revopp[21]; X char testsignal[25]; X char opprevsig[25]; X char space[80]; X X clrscr(); X getseqfilename(); X clrscr(); X savename(); X clrscr(); X sigclass(); X X for (m = 0; m < seqcount; m++) /* Used to strip \n's from seq X lines in text file*/ X seq[m][strlen(seq[m]) - 1] = '\0'; X X for (m = 0; m < seqcount; m++) /* Concat's seq. lines from seq X file into same array line*/ X strcat(sequence, seq[m]); X X clrscr(); X basepairs = strlen(sequence); X printf("%s: %4d base pairs", SEQFILE, basepairs); X printf(" Signal database file: %s\n", SIGNALX); X printf(" < = Reverse Opposite Strand\n\n"); X X /* Open the save file in append mode. */ X X sigwrite = fopen(SAVEFILE, "at"); X X /* Write the name of the signal to a file */ X X fprintf(sigwrite, "%s: %4d base pairs", SEQFILE, basepairs); X fprintf(sigwrite, " Signal database file: %s\n", SIGNALX); X fprintf(sigwrite, " < = Reverse Opposite Strand\n\n"); X fclose(sigwrite); X X X sigcount = getsignals(); X X i = 0; /* Reset i to zero for next comparison. */ X do /* Compare to search sequence. */ X { X if(i % 50 == 0) X { X printf("\n\n"); X strcpy(map, &sequence[i]); X map[50] = '\0'; X printf("%-7d%s", i + 1, map); X sigwrite = fopen(SAVEFILE, "a+t"); X fprintf(sigwrite, "\n\n"); X fprintf(sigwrite, "%-7d%s", i + 1, map); X fclose(sigwrite); X } X for (j = 0; j < sigcount; j++) /* For each signal sequence:*/ X { X X strcpy(testsignal, sigarray[j].sigseq); /* Make working copy of signal seq*/ X testsignal[sigarray[j].siglen] = '\0'; X X result = compare(&sequence[i], testsignal); X if (result == 0) X { X printf("\n"); X strcpy(space, " \0"); X space[((i % 50) + 7)] = '\0'; X printf("%s", space); X printf("%s", sigarray[j].signame); X X /* Open the save file in append mode. */ X X sigwrite = fopen(SAVEFILE, "a+t"); X X /* Write the name of the signal to a file */ X fprintf(sigwrite, "\n"); X fprintf(sigwrite, "%s", space); X fprintf(sigwrite, "%s", sigarray[j].signame); X X fclose(sigwrite); X X } X X strcpy(opprevsig, testsignal); X for (p = strlen(testsignal) - 1, q = 0; q < strlen(testsignal); p--, q++) X { X if (testsignal[p] == 'A') X opprevsig[q] = 'T'; X X else if (testsignal[p] == 'T') X opprevsig[q] = 'A'; X X else if (testsignal[p] == 'C') X opprevsig[q] = 'G'; X X else if (testsignal[p] == 'G') X opprevsig[q] = 'C'; X X else if (testsignal[p] == 'R') X opprevsig[q] = 'Y'; X X else if (testsignal[p] == 'Y') X opprevsig[q] = 'R'; X X else if (testsignal[p] == 'M') X opprevsig[q] = 'K'; X X else if (testsignal[p] == 'K') X opprevsig[q] = 'M'; X X X else if (testsignal[p] == 'D') X opprevsig[q] = 'H'; X X else if (testsignal[p] == 'H') X opprevsig[q] = 'D'; X X else if (testsignal[p] == 'B') X opprevsig[q] = 'V'; X X else if (testsignal[p] == 'V') X opprevsig[q] = 'B'; X X } X X X result = compare(&sequence[i], opprevsig); X X if (result == 0) X { X strcpy(revopp, sigarray[j].signame); X for(k = 0; k < (strlen(revopp)); k++) X { X if( revopp[k] == ' ' && revopp[k+1] == ' ') X revopp[k] = '\0'; X } X strcat(revopp, "<\0"); X X strcpy(space, " \0"); X space[((i % 50) + 7)] = '\0'; X X printf("\n"); X printf("%s", space); X printf("%s", revopp); X X /* Open the save file in append mode. */ X X sigwrite = fopen(SAVEFILE, "a+t"); X X /* Write the name of the signal to a file */ X fprintf(sigwrite, "\n"); X fprintf(sigwrite, "%s", space); X fprintf(sigwrite, "%s", revopp); X X X fclose(sigwrite); X } X } X } X while (sequence[i++] != '\0'); X X printf("\n\n\n\nRESULTS OF SEARCH SENT TO FILE: %s", SAVEFILE); X printf("\n\nEND OF SEARCH\n\n"); X X } /* END OF MAIN */ X Xint getsignals() X { X FILE *sigread; X int sigcount = 0; /* counts the number of signals in the file*/ X char strlen[TEMPLEN]; /* templen holds siglen for atoi conversion */ X X sigread = fopen(SIGNALX, "rt"); X X X X /* if file exists, read its contents. */ X X if (sigread != NULL) X { X /* Stop reading at MAXSIG or end of file. */ X X while ((sigcount < MAXSIG) && X (fgets(sigarray[sigcount].signame, NAMELEN, X sigread) != NULL)) X { X X /* Read the signal sequence. */ X X fgets(sigarray[sigcount].sigseq, SEQLEN, sigread); X X X /* Read the signal length as a string value, and X then use atoi to convery the string to a int val*/ X X fgets(strlen, TEMPLEN, sigread); X sigarray[sigcount++].siglen = atoi(strlen); X X } X fclose(sigread); X } X return(sigcount); X } Xvoid getseq() X { X int z; X seqcount = 0; X seqread = fopen(SEQFILE, "rt"); X if (seqread != NULL) X { X while ((seqcount < FILELEN) && X (fgets(seq[seqcount], TEMPLEN, seqread) != NULL)) X { X if(isupper(seq[seqcount][0]) == 0) X { X for(z = 0; z < strlen(seq[seqcount]); z++) X { X seq[seqcount][z] = toupper(seq[seqcount][z]); X } X } X seqcount++; X } X fclose(seqread); X seqcount = seqcount; X X } X else /*if no seqfile is found*/ X { X clrscr(); X printf("FILE NOT FOUND\n"); X printf("Make sure file is in current directory\n"); X printf("Make sure you included the file extension\n"); X pause(); X clrscr(); X getseqfilename(); X } X } X Xvoid getseqfilename() X { X CUR_MOVE(11,25); X X printf("\033[1m"); X printf("Sequence file name? "); X printf("\033[0m"); X printf("\033[1m"); X gets(SEQFILE); X printf("\033[0m"); X getseq(); X } X X Xint compare(window, testsignal) Xchar window[]; Xchar testsignal[]; X{ X int i, result = 0; X X for (i = 0; i < strlen(testsignal); i++) X { X if (result == 1) X break; X X X X if (testsignal[i] == window[i] ) X result += 0; X X else if (testsignal[i] == 'N' && window[i] == 'A' || X testsignal[i] == 'N' && window[i] == 'T' || X testsignal[i] == 'N' && window[i] == 'C' || X testsignal[i] == 'N' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'R' && window[i] == 'A' || X testsignal[i] == 'R' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'Y' && window[i] == 'C' || X testsignal[i] == 'Y' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'M' && window[i] == 'A' || X testsignal[i] == 'M' && window[i] == 'C') X result += 0; X X else if (testsignal[i] == 'W' && window[i] == 'A' || X testsignal[i] == 'W' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'S' && window[i] == 'C' || X testsignal[i] == 'S' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'K' && window[i] == 'G' || X testsignal[i] == 'K' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'D' && window[i] == 'A' || X testsignal[i] == 'D' && window[i] == 'G' || X testsignal[i] == 'D' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'H' && window[i] == 'A' || X testsignal[i] == 'H' && window[i] == 'C' || X testsignal[i] == 'H' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'V' && window[i] == 'A' || X testsignal[i] == 'V' && window[i] == 'C' || X testsignal[i] == 'V' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'B' && window[i] == 'C' || X testsignal[i] == 'B' && window[i] == 'G' || X testsignal[i] == 'B' && window[i] == 'T') X result += 0; X X X else result = 1; X } /* end of if */ X return(result); X X} /* end of compare */ X X Xvoid savename() X { X CUR_MOVE(11, 25); X printf("\033[1m"); X printf("File name to SAVE results? "); X printf("\033[0m"); X printf("\033[1m"); X gets(SAVEFILE); X printf("\033[0m"); X X } X X Xvoid sigclass() X{ X char response; X display(); X X /*Get the user's choice, convert it to X uppercase, and display it on the screen. */ X response = getchar(); X response = toupper(response); X X /* select the signalx.dat file */ X X switch(response) X { X case 'M' : X strcpy(SIGNALX, "mammal.dat"); X break; X X case 'B' : X strcpy(SIGNALX, "bird.dat"); X break; X X case 'X' : X strcpy(SIGNALX, "xenopus.dat"); X break; X X case 'D' : X strcpy(SIGNALX, "dros.dat"); X break; X X case 'Y' : X strcpy(SIGNALX, "yeast.dat"); X break; X X case 'G' : X strcpy(SIGNALX, "tfd.dat"); X break; X X case 'K' : X strcpy(SIGNALX, "user.dat"); X system(USER); X pause; X break; X X } X} /*end of sigclass()*/ X X/* The display function displays the menu on the screen. */ Xvoid display() X { X printf("\033[7m"); X CUR_MOVE(6, 25); X printf("SELECT SIGNAL CLASS"); X printf("\033[0m"); X printf("\n"); X printf("\033[1m"); X printf("\n\n\t\t\tM"); X printf("\033[0m"); X printf("ammal"); X printf("\033[1m"); X printf("\n\n\t\t\tB"); X printf("\033[0m"); X printf("ird"); X printf("\033[1m"); X printf("\n\n\t\t\tA"); X printf("\033[0m"); X printf("mphibian"); X printf("\033[1m"); X printf("\n\n\t\t\tI"); X printf("\033[0m"); X printf("nsect"); X printf("\033[1m"); X printf("\n\n\t\t\tY"); X printf("\033[0m"); X printf("east"); X printf("\033[1m"); X printf("\n\n\t\t\tG"); X printf("\033[0m"); X printf("hosh TFD"); X printf("\033[1m"); X printf("\n\n\t\t\tK"); X printf("\033[0m"); X printf("eyboard entry\n\n"); X printf("CHOICE = "); X X X } /* end of display */ X X X/* The pause function creates a pause in the action so the X user can examine the output screen. */ X Xvoid pause() X { X printf("\033[7m"); X printf("Press a key..."); X printf("\033[0m"); X getchar(); X X } /* end of pause */ X X X/* END */ END_OF_FILE if test 12273 -ne `wc -c <'scanm.c'`; then echo shar: \"'scanm.c'\" unpacked with wrong size! fi # end of 'scanm.c' fi if test -f 'scans.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'scans.c'\" else echo shar: Extracting \"'scans.c'\" \(9262 characters\) sed "s/^X//" >'scans.c' <<'END_OF_FILE' X/* SCANS.C UNIX.*/ X X#include X#include X#include X#include "ansi.h" X X#define USER "USERSIG" X#define MAXSIG 2000 X#define NAMELEN 21 X#define SEQLEN 26 X#define TEMPLEN 81 X#define SEQUENCE 100000 X#define FILELEN 1250 X#define clrscr() printf("%c%c%c%c", 27, 91, 50, 74) X Xint getsignals(); Xvoid getseqfilename(); Xvoid getseq(); Xvoid savename(); Xvoid sigclass(); Xvoid display(); Xint compare(); Xvoid pause(); X Xstruct sigstruct X { X char signame[NAMELEN]; X char sigseq[SEQLEN]; X int siglen; X X } sigarray[MAXSIG]; X Xchar seq[FILELEN][TEMPLEN]; Xchar SEQFILE[13]; Xchar SAVEFILE[13]; Xchar SIGNALX[13]; Xchar sequence[SEQUENCE]; Xchar window[SEQUENCE]; Xchar testsignal[25]; Xchar opprevsig[25]; XFILE *sigread; XFILE *seqread; XFILE *sigwrite; Xint seqcount; Xint sigcount; X Xmain() X { X register int i, j, m, p, q; X int result, basepairs; X X clrscr(); X getseqfilename(); X clrscr(); X savename(); X clrscr(); X sigclass(); X X X for (m = 0; m < seqcount; m++) X seq[m][strlen(seq[m]) - 1] = '\0'; X X for (m = 0; m < seqcount; m++) X strcat(sequence, seq[m]); X X clrscr(); X basepairs = strlen(sequence); X printf("%s: %4d base pairs", SEQFILE, basepairs); X printf(" Signal database file: %s\n\n", SIGNALX); X printf("SIGNAL NAME SIGNAL SEQ. SEARCH SEQ., 1ST bp of signal\n"); X printf("____________________________________________________________________________\n"); X X sigwrite = fopen(SAVEFILE, "at"); X X fprintf(sigwrite, "%s: %4d base pairs", SEQFILE, basepairs); X fprintf(sigwrite, " Signal database file: %s\n\n", SIGNALX); X fprintf(sigwrite, "SIGNAL NAME SIGNAL SEQ. SEARCH SEQ., 1ST bp of signal\n"); X fprintf(sigwrite, "____________________________________________________________________________\n"); X X fclose(sigwrite); X X getsignals(); Xprintf("sigcount = %d\n", sigcount); X for (j = 0; j < sigcount; j++) X { X i = 0; X X strcpy(testsignal, sigarray[j].sigseq); X strcpy(opprevsig, testsignal); X for (p = strlen(testsignal) - 1, q = 0; q < strlen(testsignal); p--, q++) X { X if (testsignal[p] == 'A') X opprevsig[q] = 'T'; X X else if (testsignal[p] == 'T') X opprevsig[q] = 'A'; X X else if (testsignal[p] == 'C') X opprevsig[q] = 'G'; X X else if (testsignal[p] == 'G') X opprevsig[q] = 'C'; X X else if (testsignal[p] == 'R') X opprevsig[q] = 'Y'; X X else if (testsignal[p] == 'Y') X opprevsig[q] = 'R'; X X X else if (testsignal[p] == 'M') X opprevsig[q] = 'K'; X X else if (testsignal[p] == 'K') X opprevsig[q] = 'M'; X X else if (testsignal[p] == 'D') X opprevsig[q] = 'H'; X X else if (testsignal[p] == 'H') X opprevsig[q] = 'D'; X X else if (testsignal[p] == 'B') X opprevsig[q] = 'V'; X X else if (testsignal[p] == 'V') X opprevsig[q] = 'B'; X X } X X do /* Compare to search sequence. */ X { X X result = compare(&sequence[i], testsignal); X if (result == 0) X { X printf("%s: %-25s: %4d\n", sigarray[j].signame, X sigarray[j].sigseq, i + 1); X sigwrite = fopen(SAVEFILE, "at"); X fprintf(sigwrite, "%s: %-25s: %4d%\n", X sigarray[j].signame,sigarray[j].sigseq, i + 1); X fclose(sigwrite); X } X result = compare(&sequence[i], opprevsig); X if (result == 0) X { X printf("%s: %-25s: %4d Reverse opposite strand\n", sigarray[j].signame, X sigarray[j].sigseq, i + 1); X sigwrite = fopen(SAVEFILE, "at"); X fprintf(sigwrite, "%s: %-25s: %4d Reverse opposite strand\n", X sigarray[j].signame,sigarray[j].sigseq, i + 1); X fclose(sigwrite); X } X } X while (sequence[i++] != '\0'); X } X printf("\nRESULTS OF SEARCH SENT TO FILE: %s\n", SAVEFILE); X printf("END OF SEARCH\n\n"); X } /* END OF MAIN */ X Xint getsignals() X { X char strlen[TEMPLEN]; /* templen holds siglen for atoi conversion */ X sigcount = 0; /* counts the number of signals in the file*/ X sigread = fopen(SIGNALX, "rt"); X X if (sigread != NULL) X { X while ((sigcount < MAXSIG) && X (fgets(sigarray[sigcount].signame, NAMELEN, X sigread) != NULL)) X { X fgets(sigarray[sigcount].sigseq, SEQLEN, sigread); X X fgets(strlen, TEMPLEN, sigread); X sigarray[sigcount].siglen = atoi(strlen); X sigarray[sigcount].sigseq[sigarray[sigcount++].siglen] = '\0'; X } X fclose(sigread); X } X } X Xvoid getseq() X { X int z; X seqcount = 0; X seqread = fopen(SEQFILE, "rt"); X if (seqread != NULL) X { X while ((seqcount < FILELEN) && X (fgets(seq[seqcount], TEMPLEN, seqread) != NULL)) X { X if(isupper(seq[seqcount][0]) == 0) X { X for(z = 0;z < strlen(seq[seqcount]); z++) X { X seq[seqcount][z] = toupper(seq[seqcount][z]); X } X } X seqcount++; X } X fclose(seqread); X seqcount = seqcount; X } X else /*if no seqfile is found*/ X { X clrscr(); X printf("FILE NOT FOUND\n"); X printf("Make sure file is in current directory\n"); X printf("Make sure you included the file extension\n"); X pause(); X clrscr(); X getseqfilename(); X } X X } X X Xint compare(window, testsignal) Xchar window[]; Xchar testsignal[]; X{ X int i, result = 0; X X for (i = 0; i < strlen(testsignal); i++) X { X if (result == 1) X break; X X if (testsignal[i] == window[i]) X result += 0; X X else if (testsignal[i] == 'N' && window[i] == 'A' || X testsignal[i] == 'N' && window[i] == 'T' || X testsignal[i] == 'N' && window[i] == 'C' || X testsignal[i] == 'N' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'R' && window[i] == 'A' || X testsignal[i] == 'R' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'Y' && window[i] == 'C' || X testsignal[i] == 'Y' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'M' && window[i] == 'A' || X testsignal[i] == 'M' && window[i] == 'C') X result += 0; X X else if (testsignal[i] == 'W' && window[i] == 'A' || X testsignal[i] == 'W' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'S' && window[i] == 'C' || X testsignal[i] == 'S' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'K' && window[i] == 'G' || X testsignal[i] == 'K' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'D' && window[i] == 'A' || X testsignal[i] == 'D' && window[i] == 'G' || X testsignal[i] == 'D' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'H' && window[i] == 'A' || X testsignal[i] == 'H' && window[i] == 'C' || X testsignal[i] == 'H' && window[i] == 'T') X result += 0; X X else if (testsignal[i] == 'V' && window[i] == 'A' || X testsignal[i] == 'V' && window[i] == 'C' || X testsignal[i] == 'V' && window[i] == 'G') X result += 0; X X else if (testsignal[i] == 'B' && window[i] == 'C' || X testsignal[i] == 'B' && window[i] == 'G' || X testsignal[i] == 'B' && window[i] == 'T') X result += 0; X X else result = 1; X } /* end of if */ X return(result); X X} /* end of compare */ X Xvoid sigclass() X{ X char response; X display(); X response = getchar(); X response = toupper(response); X X switch(response) X { X case 'M' : X strcpy(SIGNALX, "mammal.dat"); X break; X X case 'B' : X strcpy(SIGNALX, "bird.dat"); X break; X X case 'X' : X strcpy(SIGNALX, "xenopus.dat"); X break; X X case 'D' : X strcpy(SIGNALX, "dros.dat"); X break; X X case 'Y' : X strcpy(SIGNALX, "yeast.dat"); X break; X X case 'G' : X strcpy(SIGNALX, "tfd.dat"); X break; X X case 'K' : X strcpy(SIGNALX, "user.dat"); X system(USER); X pause; X break; X X } getchar(); X} /*end of sigclass()*/ X Xvoid getseqfilename() X { X CUR_MOVE(11,25); X X printf("\033[1m"); X printf("Sequence file name? "); X printf("\033[0m"); X printf("\033[1m"); X gets(SEQFILE); X printf("\033[0m"); X getseq(); X } X Xvoid savename() X { X CUR_MOVE(11, 25); X printf("\033[1m"); X printf("File name to SAVE results? "); X printf("\033[0m"); X printf("\033[1m"); X gets(SAVEFILE); X printf("\033[0m"); X X } X X X/* The display function displays the menu on the screen. */ Xvoid display() X { X printf("\033[7m"); X CUR_MOVE(6, 25); X printf("SELECT SIGNAL CLASS"); X printf("\033[0m"); X printf("\n"); X printf("\033[1m"); X printf("\n\n\t\t\tM"); X printf("\033[0m"); X printf("ammal"); X printf("\033[1m"); X printf("\n\n\t\t\tB"); X printf("\033[0m"); X printf("ird"); X printf("\033[1m"); X printf("\n\n\t\t\tA"); X printf("\033[0m"); X printf("mphibian"); X printf("\033[1m"); X printf("\n\n\t\t\tI"); X printf("\033[0m"); X printf("nsect"); X printf("\033[1m"); X printf("\n\n\t\t\tY"); X printf("\033[0m"); X printf("east"); X printf("\033[1m"); X printf("\n\n\t\t\tG"); X printf("\033[0m"); X printf("hosh TFD"); X printf("\033[1m"); X printf("\n\n\t\t\tK"); X printf("\033[0m"); X printf("eyboard entry\n\n"); X printf("CHOICE = "); X X X } /* end of display */ X X X/* The pause function creates a pause in the action so the X user can examine the output screen. */ X Xvoid pause() X { X printf("\033[7m"); X printf("Press a key..."); X printf("\033[0m"); X getchar(); X X } /* end of pause */ X X X/* END */ END_OF_FILE if test 9262 -ne `wc -c <'scans.c'`; then echo shar: \"'scans.c'\" unpacked with wrong size! fi # end of 'scans.c' fi if test -f 'signal.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'signal.c'\" else echo shar: Extracting \"'signal.c'\" \(3382 characters\) sed "s/^X//" >'signal.c' <<'END_OF_FILE' X/* PATTERN.C Display a menu offering a selection of activities. Runs X the following: SCANxx.C, TITLE.C, PATSCAN.C*/ X X#include X#include X#include "ansi.h" X X#define ZERO 0 X#define ONE 1 X#define clrscr() printf("%c%c%c%c", 27, 91, 50, 74) X X X#define TITLE "title" X#define SCANL "scanl" X#define SCANS "scans" X#define SCANM "scanm" X#define PROG "program" X#define FORM "format" X#define RESULTS "interp" X#define USE "user" X#define RUN "running" X Xvoid display(); Xvoid pause(); X Xmain() X { X char response; /* The single-character menu choice. */ X int done = ZERO X; /* TRUE at end of performance. */ X X system(TITLE); X pause(); X X do X { X display(); X X /*Get the user's choice, convert it to X uppercase, and display it on the screen. */ X X response = getchar(); X if(isupper(response) == 0) X response = toupper(response); X /* Run the selected program. */ X X switch (response) X { X case 'L' : X system(SCANL); X getchar(); X pause(); X break; X X case 'S' : X system(SCANS); X getchar(); X pause(); X break; X X case 'M' : X system(SCANM); X getchar(); X pause(); X break; X X case 'B' : X system(PROG); X getchar(); X pause(); X break; X X case 'F' : X system(FORM); X getchar(); X pause(); X break; X X case 'R' : X system(RUN); X getchar(); X pause(); X break; X X case 'I' : X system(RESULTS); X getchar(); X pause(); X break; X X X case 'U' : X system(USE); X getchar(); X pause(); X break; X X X case 'Q' : X clrscr(); X done = ONE; X X } X } X while (!done); X X } /* end of main() */ X X/* The display function displays the menu on the screen. */ X Xvoid display() X { X clrscr(); X printf("\n\n"); X printf("\033[7m"); X printf(" S I G N A L S C A N "); X X printf("\n\n"); X printf(" MENU "); X printf("\033[0m"); X printf("\n"); X printf("\033[1m"); X printf("\n\t\tS"); X printf("\033[0m"); X printf("ignal group scan (FASTEST)"); X printf("\033[1m"); X printf("\n\t\tL"); X printf("\033[0m"); X printf("inear sequence scan"); X printf("\033[1m"); X printf("\n\t\tM"); X printf("\033[0m"); X printf("ap signal scan"); X printf("\033[1m"); X printf("\n\t\tQ"); X printf("\033[0m"); X printf("uit."); X printf("\n"); X X printf("\n"); X printf("\033[7m"); X printf("\n\n\n"); X printf(" HELP "); X printf("\033[0m"); X printf("\n"); X printf("\033[1m"); X printf("\n\t\tB"); X printf("\033[0m"); X printf("eginning SIGNAL SCAN"); X printf("\033[1m"); X printf("\n\t\tF"); X printf("\033[0m"); X printf("ormat of sequence"); X printf("\033[1m"); X printf("\n\t\tR"); X printf("\033[0m"); X printf("unning SIGNAL SCAN"); X printf("\033[1m"); X printf("\n\t\tI"); X printf("\033[0m"); X printf("nterpreting results"); X printf("\033[1m"); X printf("\n\t\tU"); X printf("\033[0m"); X printf("ser information\n\n"); X X printf("\033[7m"); X printf(" ENTER FIRST LETTER "); X printf("\033[0m"); X X } /* end of display */ X X/* The pause function creates a pause in the action so the X user can examine the output screen. */ X Xvoid pause() X { X CUR_MOVE(24, 2); X printf("\033[7m"); X printf(" Press return to see menu... "); X printf("\033[0m"); X getchar(); X X X } /* end of pause */ X X X X END_OF_FILE if test 3382 -ne `wc -c <'signal.c'`; then echo shar: \"'signal.c'\" unpacked with wrong size! fi # end of 'signal.c' fi if test -f 'signal.lst' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'signal.lst'\" else echo shar: Extracting \"'signal.lst'\" \(260 characters\) sed "s/^X//" >'signal.lst' <<'END_OF_FILE' Xreadme.doc XMakefile Xansi.h Xtfd.dat Xbird.dat Xdros.dat Xformat Xformat.txt Xinterp Xinterp.txt Xmammal.dat Xprogram Xprogram.txt Xrunning Xrunning.txt Xsample.seq Xscanl.c Xscanm.c Xscans.c Xsignal.c Xsignal.lst Xsigref.doc Xtitle.c Xuser Xuser.txt Xusersig.c Xxenopus.dat Xyeast.dat END_OF_FILE if test 260 -ne `wc -c <'signal.lst'`; then echo shar: \"'signal.lst'\" unpacked with wrong size! fi # end of 'signal.lst' fi if test -f 'sigref.doc' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'sigref.doc'\" else echo shar: Extracting \"'sigref.doc'\" \(7794 characters\) sed "s/^X//" >'sigref.doc' <<'END_OF_FILE' X REFERENCES X XReference Number :1 XMitchell,P.J., Tjian,R. XTranscriptional regulation in mammalian cells by sequence-specific XDNA binding proteins XScience 245:371-378, 1989 X X XReference Number :2 XKozak,M. XPoint mutations define a sequence flanking the AUG initiator codon Xthat modulates translation by eukaryotic ribosomes XCell 44:283-292, 1986 X X XReference Number :3 XSharp,P.A. XSplicing of messenger RNA precursors XScience 235:766-771, 1987 X X XReference Number :4 XMorgan,W.D., Williams,G.T., Morimoto,R.I., Greene,J., Kingston,R.E., XTjian,R. XTwo transcriptional activators, CCAAT-box-binding transcription factor Xand heat shock transcription factor, interact with a human hsp70 Xgene promoter XMol.Cell Biol. 7:1129-1138, 1987 X X XReference Number :5 XWu,B.J., Williams,G.T., Morimoto,R.I. XDetection of three protein binding sites in the serum-regulated promoter Xof the human gene encoding the 70-kDa heat shock protein XProc.Natl.Acad.Sci.U.S.A. 84:2203-2207, 1987 X X XReference Number :6 XOdenwald,W.F., Garbern,J., Arnheiter,H., Tournier Lasserve,E., Lazzarini,R.A. XThe Hox 1.3 homeo box gene encodes a sequence specific DNA binding Xphosphoprotein XGenes Dev. 1:482-496, 1987 X X XReference Number :7 XJones,N.C., Rigby,P.W.J., Ziff,E.B. XTrans-acting protein factors and the regulation of eukaryotic tanscription: Xlessons from studies on DNA tumor viruses XGenes.Dev. 2:267-281, 1988 X X XReference Number :8 XUmesono,K., Giguere,V., Glass,C.K., Rosenfeld,M.G., Evans,R.M. XRetinoic acid and thyroid hormone induce gene expression through Xa common responsive element XNature 336:262-265, 1988 X X XReference Number :9 XBiedenkapp,H., Borgmeyer,U., Sippel,A.E., Klempnauer,K. XViral myb oncogene encodes a sequence-specific DNA-binding activity XNature 335:835-837, 1988 X X XReference Number :10 XDynan,W.S., Tjian,R. XControl of eukaryotic messenger RNA synthesis by sequence- specific XDNA-binding proteins XNature 316:774-778, 1985 X X XReference Number :11 XWingender,W. XCompilation of transcription regulating proteins XNAR 16:1879-1902, 1988 X X XReference Number :12 XClaverie,J., Sauvaget,I. XAssessing the biological significance of primary structure consensus Xpatterns using sequence databanks. I. Heat-shock and glucocorticoid Xcontrol elements in eukaryotic promoters XCABIOS 1:95-104, 1985 X X XReference Number :13 XKudo,M., Iida,Y., Shimbo,M. XSyntactic pattern analysis of 5' -splice site sequences of mRNA precursors Xin higher eukaryote genes XCABIOS 4:319-324, 1987 X X XReference Number :14 XSassone-Corsi,P., Sisson,J.C., Verma,I.M. XTranscriptional autoregulation of the proto-oncogene fos XNature 334:314-319, 1988 X X XReference Number :15 XMiyamoto,N. XGENBANK ACCESSION #Y00474, Beta Actin promoter sequence annotation Xsite table X X XReference Number :16 XLewin,B. XGenes II X2nd Edition. Wiley, New York, 1985 X X XReference Number :17 XMignotte,V., Eleouet,J.F., Raich,M., Romeo,P. XCis- and trans-acting elements involved in the regulation of the Xerythroid promoter of the human prophobilinogen deaminse gene XProc.Natl.Acad.Sci.USA 86:6548-6552, 1989 X X XReference Number :18 XComb,M., Mermod,N., Hyman,S.E., Pearlberg,J., Ross,M.E., Goodman,H.M. XProteins bound at adjacent DNA elements act synergistically to regulate Xhuman proenkephalin cAMP inducible transcription XEMBO.J. 7:3793-3805, 1988 X X XReference Number :19 XSchule,R., Muller,M., Kaltschmidt,C., Renkawitz,R. XMany transcription factors interact synergistically with steroid Xreceptors XScience 242:1418-1420, 1988 X X XReference Number :20 XRuskin,B., Krainer,A.R., Maniatis,T., Green,M.R. XExcision of an intact intron as a novel lariat structure during pre-mRNA Xsplicing in vitro XCell 38:317-331, 1984 X X XReference Number :21 XShaw,G., Kamen,R. XA conserved AU sequence from the 3' untranslated region of GM-CSF XmRNA mediates selective mRNA degradation XCell 46:659-667, 1986 X X XReference Number :22 XDriever,W., Nusslein-Volhard,C. XThe bicoid protein is a positive regluator of hunchback transcription Xin the early Drosophila embryo XNature 337:138-143, 1989 X X XReference Number :23 XHan,K., Levine,M.S., Manley,J.L. XSynergistic activation and repression of transcription by Drosophila Xhomeobox proteins XCell 56:573-583, 1989 X X XReference Number :24 XJaynes,J.B., O'Farrell,P.H. XActivation and repression of transcription by homoeodomain-containing Xproteins that bind a common site. XNature 336:744-749, 1988 X X XReference Number :25 XBiggin,M.D., Tjian,R. XA purified Drosophila homeodomain protein represses transcription Xin vitro XCell 58:433-440, 1989 X X XReference Number :26 XMihara,H., Kaiser,E.T. XA chemically synthesized Antennapedia homeo domain binds to a specific XDNA sequence XScience 242:925-927, 1988 X X XReference Number :27 XHoey,T., Warrior,R., Manak,J., Levine,M.S. XDNA-binding activities of the Drosophila melanogaster even-skipped Xprotein are mediated by its homeo domain and influenced by protein Xcontext XMol.Cell Biol. 8:4598-4607, 1988 X X XReference Number :28 XDesplan,C., Theis,J., O'Farrell,P.H. XThe sequence specificity of homeodomain-DNA interaction XCell 54:1081-1090, 1988 X X XReference Number :29 XShore,D., Nasmyth,K. XPurification and cloning of a DNA binding protein from yeast that Xbinds to both silencer and activator elements XCell 51:721-732, 1987 X X XReference Number :30 XBeachy,P.A., Krasnow,M.A., Gavis,E.R., Hogness,D.S. XAn ultrabithorax protein binds sequences near its own and the antennapedia XP1 promoters. XCell 55:1069-1081, 1988 X X XReference Number :31 XHope,I.A., Struhl,K. XGCN4, a eukaryotic transcriptional activator protein, binds as a Xdimer to target DNA XEMBO.J. 6:2781-2784, 1987 X X XReference Number :32 XBaum,J.A., Geever,R., Giles,N.H. XExpression of qa-1F activator protein: identification of upstream Xbinding sites in the qa gene cluster and localization of the DNA-binding Xdomain XMol.Cell Biol. 7:1256-1266, 1987 X X XReference Number :33 XBender,A., Sprague,G.F. XMAT alpha 1 protein, a yeast transcription activator binds synergistically Xwith a second protein to a set of cell-type-specific genes XCell 50:681-691, 1987 X X XReference Number :34 XArndt,K., Fink,G.R. XGCN4 protein, a positive transcription factor in yeast, binds general Xcontrol promoters at all 5' TGACTC 3' sequences XProc.Natl.Acad.Sci.USA 83:8516-8520, 1986 X X XReference Number :35 XJohnson,A.D., Herskowitz,I. XA repressor (MAT alpha 2 Product) and its operator control expression Xof a set of cell type specific genes in yeast XCell 42:237-247, 1985 X X XReference Number :36 XWilliams,T., Admon,A., Luscher,B., Tjian,R. XCloning and expression of AP-2, a cell-type-specific transcription Xfactor that activates inducible enhancer elements XGenes.Dev. 2:1557-1569, 1988 X X XReference Number :37 XLandschulz,W.H., Johnson,P.F., Adashi,E.Y., Graves,B.J., McKnight,S. XIsolation of a recombinant copy of the gene encoding C/EBP XGenes.Dev. 2:786-800, 1988 X X XReference Number :38 XMiyamoto,M., Fujita,T., Kimura,Y., Maruyama,M., Harada,H., Sudo,Y., XMiyata,T., Taniguchi,T. XRegulated expression of a gene encoding a nuclear fator, IFR-1, that Xspecifically binds to IFN-beta gene regulatory elements XCell 54:903-913, 1988 X X XReference Number :39 XNorman,C., Runswick,M., Pollock,R., Treisman,R. XIsolation and properties of cDNA clones encoding SRF, a transcription Xfactor that binds to the c-fos serum response element XCell 55:989-1003, 1988 X X XReference Number :40 XAmin,J., Mestril,R., Schiller,P., Dreano,M., Voellmy,R. XOrganization of the Drosophila melanogaster hsp70 heat shock regulation Xunit XMol.Cell Biol. 7:1055-1062, 1987 X X XReference Number :41 XCavener,D.R. XComparison of the consensus sequence flanking translational start Xsites in Drosophila and vertebrates XNAR 15:1353-1359, 1987 X X XReference Number :42 XPelham,H.R.B., Bienz,M. XA synthetic heat-shock promoter element confers heat-inducibility Xon the herpes simplex virus thymidine kinase gene XEMBO.J. 1:1473-1477, 1982 END_OF_FILE if test 7794 -ne `wc -c <'sigref.doc'`; then echo shar: \"'sigref.doc'\" unpacked with wrong size! fi # end of 'sigref.doc' fi if test -f 'title.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'title.c'\" else echo shar: Extracting \"'title.c'\" \(1269 characters\) sed "s/^X//" >'title.c' <<'END_OF_FILE' X/* TITLE.C is a title page for SIGSCANX.C */ X X#include X#include "ansi.h" X X X#define clrscr() printf("%c%c%c%c", 27, 91, 50, 74) X Xvoid timeloop(); X Xmain() X{ X int i = 0; X clrscr(); X printf("\n\t\t\t Version 1.02\n"); X printf("\n\t\t\t Copyright (c) 1990"); X printf("\n\t\t\t All Rights Reserved\n"); X printf("\n\t\t\t\t by\n"); X printf("\n\t\t\t Univ. of Calif.\n\n\n\n\n"); X X do X { X CUR_MOVE(7,29); X printf("\033[1m"); X printf(" I G N A L S C A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S G N A L S C A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I N A L S C A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I G A L S C A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I G N L S C A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I G N A S C A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I G N A L C A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I G N A L S A N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I G N A L S C N"); X timeloop(); X CUR_MOVE(7,29); X printf("S I G N A L S C A "); X timeloop(); X X } X while(i++ != 3); X CUR_MOVE(7,29); X printf("S I G N A L S C A N"); X printf("\033[0m"); X} X X Xvoid timeloop() X{ X int j; X for(j = 0; j < 55000; j++) X { X X X }; X} END_OF_FILE if test 1269 -ne `wc -c <'title.c'`; then echo shar: \"'title.c'\" unpacked with wrong size! fi # end of 'title.c' fi if test -f 'user' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'user'\" else echo shar: Extracting \"'user'\" \(19 characters\) sed "s/^X//" >'user' <<'END_OF_FILE' Xclear Xcat user.txt END_OF_FILE if test 19 -ne `wc -c <'user'`; then echo shar: \"'user'\" unpacked with wrong size! fi chmod +x 'user' # end of 'user' fi if test -f 'user.txt' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'user.txt'\" else echo shar: Extracting \"'user.txt'\" \(783 characters\) sed "s/^X//" >'user.txt' <<'END_OF_FILE' X Signal scan is a program developed by Dan S. Prestridge, to facilitate the Xanalysis of DNA sequences for known eukaryotic signals. This program is free. XYou may copy and distribute this program as freely as you wish, but you may Xnot charge for its distribution. This program is copyrighted by Los Alamos XNational Laboratory and the University of California. X The source code is written in the `C' language and is fairly easy to port Xover to other hardware and operating systems. The source code will be made Xavailable upon request. X The author welcomes comments and suggestions, on the program or additions Xto the database. Please contact: X X Dan S. Prestridge X Los Alamos National Laboratory X Group T-10, MS K710 X Los Alamos, NM 87545 X X E-mail: DXP%LIFE@LANL.GOV X END_OF_FILE if test 783 -ne `wc -c <'user.txt'`; then echo shar: \"'user.txt'\" unpacked with wrong size! fi # end of 'user.txt' fi if test -f 'usersig.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'usersig.c'\" else echo shar: Extracting \"'usersig.c'\" \(3663 characters\) sed "s/^X//" >'usersig.c' <<'END_OF_FILE' X/* This file adds new signals to SIGNAL.DAT file. X USERSIG creates a user signal file. */ X X#include X#include X#include X#include "ansi.h" X X X#define HORIZ1 40 X#define HORIZ2 80 X#define VERT1 24 X#define VERT2 1 X#define HORIZBOXCHAR 205 X#define VERTBOXCHAR 186 X#define NWCORNER 201 X#define SWCORNER 200 X#define NECORNER 187 X#define SECORNER 188 X X X#define clrscr() printf("%c%c%c%c", 27, 91, 50, 74) X#define NAMELEN 20 X#define SEQLEN 26 X Xchar SIGNALX[13]; X Xvoid box(); Xvoid sigclass(); Xvoid iub(); X Xmain() X { X X FILE *sigwrite; X X char signame[NAMELEN], X sigseq[SEQLEN], X yesno, X siglenstr[SEQLEN]; /* The input signal length string */ X int siglen; /* The signal length converted to an integer */ X X clrscr(); X sigclass(); X X X X /* Open the signal file in append mode. */ X X X sigwrite = fopen(SIGNALX, "wt"); X X X /* Keep appending signals utill user stops. */ X X do X { X clrscr(); X iub(); X X /* Read the signal name. */ X X CUR_MOVE(5, 1); X printf("\033[1m"); X printf("Signal name? "); X printf("\033[0m"); X box(6, 1, 8, 22); X printf("\033[1m"); X CUR_MOVE(7, 2); X gets(signame); X printf("\033[0m"); X X /* Reads the signal sequence. */ X CUR_MOVE(10, 1); X printf("\033[1m"); X printf("Input sequence: "); X printf("\033[0m"); X box(11, 1, 13, 22); X printf("\033[1m"); X CUR_MOVE(12, 2); X gets(sigseq); X /*strupr(sigseq);*/ X printf("\033[0m"); X X X X /* Reads the signal length. */ X siglen = strlen(sigseq); X X X /* Write the name of the signal to a file */ X fprintf(sigwrite, "%-20s%-26s%-10d\n", X signame, sigseq, siglen); X X /* Finds out if there is another signal to add. */ X printf("\n\n\nAnother signal to add? "); X do X { X yesno = getchar(); X yesno = toupper(yesno); X } X while ((yesno != 'Y') && (yesno != 'N')); /* Puts computer into a loop to wait for answer */ X } X while (yesno == 'Y'); X X fclose(sigwrite); X } /* end of addsignals */ X Xvoid sigclass() X{ X X /* select the signalx.dat file */ X X strcpy(SIGNALX, "USER.DAT"); X X X X} /*end of sigclass()*/ X X X X/* The box function displays a frame box around an area of the screen. X The upper-left corner of the area is (x1, y1) and the lower-right X corner is (x2, y2). */ X Xvoid box(y1, x1, y2, x2) Xint y1; Xint x1; Xint y2; Xint x2; X { X int i; X printf("\033[7m"); X /*Draw the horizontal lines. */ X X for (i = x1; i <= x2; i++) X { X CUR_MOVE(y1, i); X putchar(HORIZBOXCHAR); X CUR_MOVE(y2, i); X putchar(HORIZBOXCHAR); X } X X /* Draw the vertical lines */ X X for (i = y1; i <= y2; i++) X { X CUR_MOVE(i, x1); X putchar(VERTBOXCHAR); X CUR_MOVE(i, x2); X putchar(VERTBOXCHAR); X } X X /* Draw the corners. */ X X CUR_MOVE(y1, x1); X putchar(NWCORNER); X CUR_MOVE(y2, x1); X putchar(SWCORNER); X CUR_MOVE(y1, x2); X putchar(NECORNER); XCUR_MOVE(y2, x2); X putchar(SECORNER); X printf("\033[0m"); X } /* end of box*/ X Xvoid iub() X{ X printf("\n\t\t\t\t\t\t R = A or G"); X printf("\n\t\t\t\t\t\t Y = C or T"); X printf("\n\t\t\t\t\t\t M = A or C"); X printf("\n\t\t\t\t\t\t W = A or T"); X printf("\n\t\t\t\t\t\t S = C or G"); X printf("\n\t\t\t\t\t\t K = G or T"); X printf("\n\t\t\t\t\t\t D = A or G or T"); X printf("\n\t\t\t\t\t\t H = A or C or T"); X printf("\n\t\t\t\t\t\t V = A or C or G"); X printf("\n\t\t\t\t\t\t B = C or G or T"); X printf("\n\t\t\t\t\t\t N = A or C or G or T"); X X box(1, 44, 13, 74); X CUR_MOVE(1, 53); X printf("\033[7m"); X printf("5"); X printf("\033[0m"); X printf("\033[1m"); X printf("IUB SYMBOLS"); X printf("\033[7m"); X printf("F"); X printf("\033[0m"); X} X X X X/* END */ X X END_OF_FILE if test 3663 -ne `wc -c <'usersig.c'`; then echo shar: \"'usersig.c'\" unpacked with wrong size! fi # end of 'usersig.c' fi if test -f 'xenopus.dat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'xenopus.dat'\" else echo shar: Extracting \"'xenopus.dat'\" \(130 characters\) sed "s/^X//" >'xenopus.dat' <<'END_OF_FILE' XOct. Binding Fact. ATGCAAATAG 10 REF 11 XSRE AAGATNNCCANATNTGGNNATCTT 24 REF 11 END_OF_FILE if test 130 -ne `wc -c <'xenopus.dat'`; then echo shar: \"'xenopus.dat'\" unpacked with wrong size! fi # end of 'xenopus.dat' fi if test -f 'yeast.dat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'yeast.dat'\" else echo shar: Extracting \"'yeast.dat'\" \(2247 characters\) sed "s/^X//" >'yeast.dat' <<'END_OF_FILE' XGAL 4 (1) AGGAAGACTCTCCTCCG 17 REF 11 XGAL 4 (2) CGCGCCGCACTGCTCCGAACAAT 23 REF 11 XGAL 4 (3) CGGATTAGAAGCCGCCG 17 REF 11 XGAL 4 (4) CGGGTGACAGCCCTCCGA 18 REF 11 XGAL 4 (5) CGGNNNANNNTNNNCCG 17 REF 11 XGAL 4 (6) GGCTCAACAGTTGTCCGAGCGCT 23 REF 11 XGAL 4 (7) GGCTCAACAGTGCTCCGAAGTAT 23 REF 11 XGAL 4-dep ANTTATAT 8 REF 11 XGCN 4 (1) ATGASTCAT 9 REF 31 XGCN 4 (2) RRTGAYTSWY 10 REF dsp/34 XHAP1 (1) GCTAATAGCGATAATAGCGAGGG 23 REF 11 XHAP1 (2) TGGCCGGGGTTTACGGACGATGA 23 REF 11 XHEAT SHOCK (1) CNNGAANNTTCNNG 14 REF 10,44 XHEAT SHOCK (2) CTNGAANNTTCNAG 14 REF 46 XHEAT SHOCK (3) CTNGAANNTTCNRR 14 REF dsp/44 XHMR/L SILENCER AAAACCCATYMAWM 14 REF dsp/29 XMAT ALPHA 2 (1) CATGTAATTACCNAATAAGGAAATT 25 REF 35 XMAT ALPHA 2 (2) YRTGTAATTACCBAWWHRGGAAATT 25 REF dsp/35 XP BOX ALPHA (1) TTTCCTAATTAGTNCN 16 REF 33 XP BOX ALPHA (2) YTTCYTMATTRGKVYH 16 REF dsp/33 XP BOX a TTTCCTTATTNGGTAA 16 REF 33 XP BOX a TTTCCYDWWTVGGTAA 16 REF dsp/33 XQ BOX (1) WCAAYRVMAS 10 REF dsp/33 XQ BOX (2) TCAATGVCAG 10 REF dsp/33 Xqa-1F (1) GGRTAARYRYTYATCC 16 REF 32 Xqa-1F (2) GGNTAADYRYTYAWCC 16 REF dsp/32 XRC1 (1) GCCGGGGTTTA 11 REF 11 XRC1 (2) TGACCGA 7 REF 11 XRC2 (1) GATGACC 7 REF 11 XRC2 (2) GCCGGGGTTTA 11 REF 11 XRC2 (3) GGCCGGGGTTTAC 13 REF 11 XRC2 (4) TGACCGA 7 REF 11 XRPG BOX (UAS) AYCCRNRCA 9 REF 29 XSBF-B TAAATATAAAA 11 REF 11 XSBF-E/RAP1 ATGGGTTTTTG 11 REF 11,29 END_OF_FILE if test 2247 -ne `wc -c <'yeast.dat'`; then echo shar: \"'yeast.dat'\" unpacked with wrong size! fi # end of 'yeast.dat' fi echo shar: End of shell archive. exit 0