From iuvax!bionet!embl.bitnet!FUCHS Mon Jun 25 09:29:36 EST 1990 Article 347 of bionet.software: Path: iuvax!bionet!embl.bitnet!FUCHS >From: FUCHS@embl.bitnet ("Rainer Fuchs ", EMBL Data Library) Newsgroups: bionet.software Subject: Molecular biological software/EMBL File Server Message-ID: <9006251324.AA12883@genbank.bio.net> Date: 25 Jun 90 12:24:00 GMT Sender: daemon@genbank.BIO.NET Lines: 412 Here is the most recent list of molecular biological software available from the EMBL File Server. Programs which have been added or updated since April are marked by an asterisk. To get information about the EMBL File Server and the software archives send a mail message to NETSERV@EMBL.BITNET containing the lines HELP HELP SOFTWARE Rainer Fuchs, Ph.D. EMBL Data Library fuchs@embl.bitnet DOS_SOFTWARE ------------ filename ALX3.UUE author Gotoh O. description Alignment of three protein or DNA sequences literatur J. Theor. Biol. 121 (1986), 327-337 filename BIGMOUTH.UUE author Jenson, H. B. description Digitized sounds and utilities for TypeSeq and DigiSeq literatur - filename CIP.UUE author Jenson, H. B. description Calculation of reaction conditions for dephosphorylation literatur - filename CLONES.UAA author Jenson, H. B. description Management of clones, strains, libraries etc. databases (Part 1 of 2) literatur BioTechniques 7 (1989), 590-592 filename CLONES.UAB author Jenson, H. B. description Management of clones, strains, libraries etc. databases (Part 2 of 2) literatur BioTechniques 7 (1989), 590-592 filename CMOLECUL.UUE author Thompson J. R. (Cedergren R.) description graphics output of PCFOLD result files literatur Nucl. Acids Res. 10 (1982), 8351-8356 filename DETAR.UUE author VALVERDE J. R. description Utility to extract .TAR files literatur - filename DIGISEQ.UUE author Jenson, H. B. description Sequence input using digitizer literatur CABIOS 4 (1988), 218 filename DNACLONE.UAA author Roy T. K. description Management of clones, strains, libraries etc. databases (Part 1 of 2) literatur CABIOS 5 (1989), 321-322 filename DNACLONE.UAB author Roy T. K. description Management of clones, strains, libraries etc. databases (Part 2 of 2) literatur CABIOS 5 (1989), 321-322 filename ELBAMAP.UUE author King G. J. description Management of electrophoresis banding patterns literatur CABIOS 5 (1989), 313-317 filename EMOLECUL.UUE author Thompson J. R. (Cedergren R.) description graphics output of PCFOLD result files literatur Nucl. Acids Res. 10 (1982), 8351-8356 *filename ESEE.UUE author CABOT E.L. description Multiple sequence editor literatur CABIOS 5 (1989), 233-234 filename EZ-FIT.UUE author Perella F. W. description Calculation of enzyme and receptor kinetics literatur Anal. Biochem. 174 (1989), 437-447 filename FAST.UUE author Facchiano, A. description Protein structure analysis literatur CABIOS 5 (1989), 299-303 filename GEL.UUE author Thompson J. R. description Calculation of DNA restriction fragment sizes literatur Anal. Biochem. 115 (81), 113-122 filename HMOLECUL.UUE author Thompson J. R. (Cedergren R.) description graphics output of PCFOLD result files literatur Nucl. Acids Res. 10 (1982), 8351-8356 filename HYDRASC.UUE author Penttila T. J. description Contour map for two polypeptide sequences. Regions with similar hydropathic properties and second. structure properties are plotted. literatur CABIOS, in prep. filename LIGATE.UUE author Jenson, H. B. description Calculation of reaction conditions for ligation literatur BioTechniques 5 (1987), 729-730 *filename MELPROT.UUE author Sikaris K. description Secondary structure prediction and plotting literatur CABIOS 5 (1989), 323 *filename MELT.UUE author Nash J.H.E. description Melting point calculation of oligonucleotides literatur - filename MOLECSRC.UUE author Thompson J. R. (Cedergren R.) description Source code for *MOLECUL.UUE literatur Nucl. Acids Res. 10 (1982), 8351-8356 filename MOTIF.UUE author Giles I. description Motif searching program literatur CABIOS 5 (1989), 227-232 *filename MULTALIN.UUE author Corpet F. description Multiple sequence alignment literatur Nucl. Acids Res. 16 (1988), 10881-10890 filename OLIGO.UUE author Beadles K. description Oligo-directed single amino acid substitution literatur - filename PATTERN.UUE author Giles I. description Pattern searching program literatur CABIOS 5 (1989), 227-232 filename PCFOLD.UUE author Zuker M. description RNA folding literatur Meth. Enzymology 180 (1989), 262-288 filename PLASMID.UUE author Lipsick J. description Plasmid drawing program (CGA card req.) literatur - filename PREDICT.UUE author Carmenes R. S. description Protein secondary structure predictions literatur Biochem. Biophy. Res. Commun. 15 (1989), 687-698 filename PRONET.UUE author Pascarella S. description Protein structure prediction with a neural network literatur CABIOS 5 (1989), 319-320 filename SDSE.UAA author Oliver J. L. description Simulation of DNA sequence evolution (Part 1 of 2) literatur CABIOS 5 (1989), 47-50 filename SDSE.UAB author Oliver J. L. description Simulation of DNA sequence evolution (Part 2 of 2) literatur CABIOS 5 (1989), 47-50 filename SEQAID.UUE author Roufa D. description DNA and protein sequence analysis package literatur - filename SIGSEQ.UUE author Popowicz A.M. description Prediction of signal sequence cleavage site literatur CABIOS 4 (1988), 405-406 *filename SUBSIS.UUE author Mandler J. description Subdirectory handling with DNASIS(tm) or PROSIS(tm) literatur CABIOS, in press filename TDALIGN.UUE author Davison D. (Thompson K.) description Sequence alignment literatur - filename TYPESEQ.UUE author Jenson, H. B. description Sequence input using keyboard literatur CABIOS 4 (1988), 218 VAX_SOFTWARE ------------ *filename AMPHI.UUE author Jaehnig F. description Prediction of membran protein structure literatur Trends in Biochemistry 3 (1990) filename BUGFIX_6_1.GCG author - description Fixes for several bugs in GCG package v6.1 literatur - *filename CD_ACCESS.UUE author Stockwell P.A. description Driver software for ISO-formatted CD-ROMs literatur - filename CLUSTAL.UUE author Higgins D. description Multiple sequence alignment literatur Gene 73 (198), 237-244 *filename FASTEMBL.COM author Sonnhammer E. L. (Clark S.) description DCL shell for facilitating EMBL Mail-FASTA access literatur - filename GCGDBASE.UUE author Rice P. description GCG extensions developed at EMBL for using new EMBL distribution format literatur - *filename GCGQUICK.UUE author Rice P. description GCG extensions developed at EMBL for speeding up QuickSearch literatur - filename GCGEMBL.UAA ASCII conversion UUE (split) author Rice P. description GCG extensions developed at EMBL (part 1 of 2) literatur - filename GCGEMBL.UAB author Rice P. description GCG extensions developed at EMBL (part 2 of 2) literatur - *filename GCGSHELLS1.TXT author Clark S. description DCL shells for many GCG programs literatur - filename GCGSHELLS2.TXT author Clark S. description DCL shells to facilitate GenBank on-line service access literatur - filename MOTIF.UUE author Giles I. description Motif searching program literatur CABIOS 5 (1989), 227-232 filename PATTERN.UUE author Giles I. description Pattern searching program literatur CABIOS 5 (1989), 227-232 *filename PROINDEX.UUE author Clark S. description Index file creation for ProSite pattern database literatur - *filename PROSITEC.UUE author Hofmann K. description Conversion of Prosite database to Find format literatur - *filename SCRUTINE.UAA author Sibbald P. description SCRUTINEER: a package for searching protein sequence databases (part 1 of 4) literatur CABIOS, in press *filename SCRUTINE.UAB author Sibbald P. description SCRUTINEER: a package for searching protein sequence databases (part 2 of 4) literatur CABIOS, in press *filename SCRUTINE.UAC author Sibbald P. description SCRUTINEER: a package for searching protein sequence databases (part 3 of 4) literatur CABIOS, in press *filename SCRUTINE.UAD author Sibbald P. description SCRUTINEER: a package for searching protein sequence databases (part 4 of 4) literatur CABIOS, in press *filename STATSRCH.UUE author Mott R. F. description Database searching taking into account the statistical significance of any similarities found literatur CABIOS, 5 (1989), 123-132 filename TREEALIG.UAA author Hein J. description Multiple sequence alignment and phylogeny (part 1 of 2) literatur Meth. Enzymol. 183, p? filename TREEALIG.UAB author Hein J. description Multiple sequence alignment and phylogeny (part 2 of 2) literatur Meth. Enzymol. 183, p? MAC_SOFTWARE ------------ filename BUFSTACK.HQX author Beynon R. J. description Calculation of thermodynamically-corrected buffer recipes literatur CABIOS 4 (1988), 487-490 filename DNAID.HQX author Dardel F. description DNA sequence editor with grep-like search routine literatur CABIOS 4 (1988), 483-486 filename DOTTYPLOT.HQX author Gilbert D. description Dot-matrix comparison of DNA sequences literatur CABIOS 6 (1990), 117 filename ENZYMEKIN.HQX author Gilbert D. description Calculation of enzyme kinetics literatur CABIOS 6 (1990), 113-116 filename GELFRAG.HQX author Gilbert D. description Calculation of DNA restriction fragment sizes literatur CABIOS 6 (1990), 113-116 filename MACDNA.HQX author Schleif R. description DNA sequence analysis, ported from IBM-PC literatur - filename MACPLASMAP.HQX author Liu J. description Plasmid drawing program. Very Mac-like! literatur - filename MACCLADE.HQX author Maddison W and Maddison D description Phylogeny program literatur - filename MATMETH.HQX author Brown J. description Molecular biological protocols literatur - filename MINIMM.HQX author Brown J. description Molecular biological protocols (more HyperCard-like) literatur - *filename READSEQ.HQX author Gilbert D. description Pascal and C routines for handling different sequence file formats (EMBL,IG,Strider etc.) literatur - filename REFSTACK.HQX author Brown J. description Management of literature references literatur - filename RRNA1.HQX author Brown J. description Phylogeny of 16/18S rRNA (part 1 of 2) literatur - filename RRNA2.HQX author Brown J. description Phylogeny of 16/18S rRNA (part 2 of 2) literatur - filename THREE.HQX author Markiewicz P. (Johnson M.) description Alignment of three protein sequences literatur -