From <@bloom-beacon.MIT.EDU:news@bloom-picayune.mit.edu> Wed Apr 8 22:21:23 1992 Received: from IUBIO.BIO.INDIANA.EDU by sunflower.bio.indiana.edu (4.1/9.5jsm) id AA07474; Wed, 8 Apr 92 22:21:16 EST Newsgroups: bionet.software.sources Path: 18.70.0.226!lfk From: lfk@eastman1.mit.edu (Lee F. Kolakowski) Subject: ProSearch 2.0 Message-Id: Sender: news@athena.mit.edu (News system) Nntp-Posting-Host: eastman1.mit.edu Organization: Mass. Inst. of Tech., Dept. of Chemistry Distribution: bionet Date: Thu, 9 Apr 1992 04:10:55 GMT Lines: 2520 Apparently-To: bionet-software-sources@bloom-beacon.mit.edu Status: R This group seems to pretty dull, lets see if we can get some more code out of those closets. :->;-)8-) Most of you are quite familiar with Amos Bairoch's ProSite Database which is now up to version 8.1. This database is a collection of sequence motifs and references which provide many potentially interesting facts on protein sequences. There are a number of programs which utilize this data. This code is the second version of ProSearch, which utilizes the ProSite database, and Awk to search for patterns in protein sequences. The previous version was supported on Unix systems, VMS systems and MSDOS systems. This code is only the Unix version. The VMS version has been made obselete by the GCG program motif. The MSDOS version of the code is becoming limited by memory in PCs. As a result, I no longer intend to deal with VMS or MSDOS support. There is a fine program called MacPattern written by Ranier Fuchs, which provides similar features to this program for Macs. This version improves the format of the output in more selectable ways, and allows the use of alternative pattern files. I'd like to thank Joe Smith (jes@mbio.med.upenn.edu) for improvements in the main searching routines. This distribution includes cregex written by Jack A.M. Leunissen. I hope this is useful to somebody out there. Frank Kolakowski ======================================================================= O Email: lfk@eastman1.mit.edu or kolakowski@helix.mgh.harvard.edu O O US Mail: Lee F. Kolakowski Endocrine Unit O O Massachusetts General Hospital Wellman 5 O O Boston, MA 02114 Phone AT&T: 1-617-726-3966 O ======================================================================= #! /bin/sh # This is a shell archive. Remove anything before this line, then unpack # it by saving it into a file and typing "sh file". To overwrite existing # files, type "sh file -c". You can also feed this as standard input via # unshar, or by typing "sh 'ProSearch2.0/COPYING' <<'END_OF_FILE' X X GNU GENERAL PUBLIC LICENSE X Version 1, February 1989 X X Copyright (C) 1989 Free Software Foundation, Inc. X 675 Mass Ave, Cambridge, MA 02139, USA X Everyone is permitted to copy and distribute verbatim copies X of this license document, but changing it is not allowed. X X Preamble X X The license agreements of most software companies try to keep users Xat the mercy of those companies. By contrast, our General Public XLicense is intended to guarantee your freedom to share and change free Xsoftware--to make sure the software is free for all its users. The XGeneral Public License applies to the Free Software Foundation's Xsoftware and to any other program whose authors commit to using it. XYou can use it for your programs, too. X X When we speak of free software, we are referring to freedom, not Xprice. Specifically, the General Public License is designed to make Xsure that you have the freedom to give away or sell copies of free Xsoftware, that you receive source code or can get it if you want it, Xthat you can change the software or use pieces of it in new free Xprograms; and that you know you can do these things. X X To protect your rights, we need to make restrictions that forbid Xanyone to deny you these rights or to ask you to surrender the rights. XThese restrictions translate to certain responsibilities for you if you Xdistribute copies of the software, or if you modify it. X X For example, if you distribute copies of a such a program, whether Xgratis or for a fee, you must give the recipients all the rights that Xyou have. You must make sure that they, too, receive or can get the Xsource code. And you must tell them their rights. X X We protect your rights with two steps: (1) copyright the software, and X(2) offer you this license which gives you legal permission to copy, Xdistribute and/or modify the software. X X Also, for each author's protection and ours, we want to make certain Xthat everyone understands that there is no warranty for this free Xsoftware. If the software is modified by someone else and passed on, we Xwant its recipients to know that what they have is not the original, so Xthat any problems introduced by others will not reflect on the original Xauthors' reputations. X X The precise terms and conditions for copying, distribution and Xmodification follow. X X GNU GENERAL PUBLIC LICENSE X TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION X X 0. This License Agreement applies to any program or other work which Xcontains a notice placed by the copyright holder saying it may be Xdistributed under the terms of this General Public License. The X"Program", below, refers to any such program or work, and a "work based Xon the Program" means either the Program or any work containing the XProgram or a portion of it, either verbatim or with modifications. Each Xlicensee is addressed as "you". X X 1. You may copy and distribute verbatim copies of the Program's source Xcode as you receive it, in any medium, provided that you conspicuously and Xappropriately publish on each copy an appropriate copyright notice and Xdisclaimer of warranty; keep intact all the notices that refer to this XGeneral Public License and to the absence of any warranty; and give any Xother recipients of the Program a copy of this General Public License Xalong with the Program. You may charge a fee for the physical act of Xtransferring a copy. X X 2. You may modify your copy or copies of the Program or any portion of Xit, and copy and distribute such modifications under the terms of Paragraph X1 above, provided that you also do the following: X X a) cause the modified files to carry prominent notices stating that X you changed the files and the date of any change; and X X b) cause the whole of any work that you distribute or publish, that X in whole or in part contains the Program or any part thereof, either X with or without modifications, to be licensed at no charge to all X third parties under the terms of this General Public License (except X that you may choose to grant warranty protection to some or all X third parties, at your option). X X c) If the modified program normally reads commands interactively when X run, you must cause it, when started running for such interactive use X in the simplest and most usual way, to print or display an X announcement including an appropriate copyright notice and a notice X that there is no warranty (or else, saying that you provide a X warranty) and that users may redistribute the program under these X conditions, and telling the user how to view a copy of this General X Public License. X X d) You may charge a fee for the physical act of transferring a X copy, and you may at your option offer warranty protection in X exchange for a fee. X XMere aggregation of another independent work with the Program (or its Xderivative) on a volume of a storage or distribution medium does not bring Xthe other work under the scope of these terms. X X 3. You may copy and distribute the Program (or a portion or derivative of Xit, under Paragraph 2) in object code or executable form under the terms of XParagraphs 1 and 2 above provided that you also do one of the following: X X a) accompany it with the complete corresponding machine-readable X source code, which must be distributed under the terms of X Paragraphs 1 and 2 above; or, X X b) accompany it with a written offer, valid for at least three X years, to give any third party free (except for a nominal charge X for the cost of distribution) a complete machine-readable copy of the X corresponding source code, to be distributed under the terms of X Paragraphs 1 and 2 above; or, X X c) accompany it with the information you received as to where the X corresponding source code may be obtained. (This alternative is X allowed only for noncommercial distribution and only if you X received the program in object code or executable form alone.) X XSource code for a work means the preferred form of the work for making Xmodifications to it. For an executable file, complete source code means Xall the source code for all modules it contains; but, as a special Xexception, it need not include source code for modules which are standard Xlibraries that accompany the operating system on which the executable Xfile runs, or for standard header files or definitions files that Xaccompany that operating system. X X 4. You may not copy, modify, sublicense, distribute or transfer the XProgram except as expressly provided under this General Public License. XAny attempt otherwise to copy, modify, sublicense, distribute or transfer Xthe Program is void, and will automatically terminate your rights to use Xthe Program under this License. However, parties who have received Xcopies, or rights to use copies, from you under this General Public XLicense will not have their licenses terminated so long as such parties Xremain in full compliance. X X 5. By copying, distributing or modifying the Program (or any work based Xon the Program) you indicate your acceptance of this license to do so, Xand all its terms and conditions. X X 6. Each time you redistribute the Program (or any work based on the XProgram), the recipient automatically receives a license from the original Xlicensor to copy, distribute or modify the Program subject to these Xterms and conditions. You may not impose any further restrictions on the Xrecipients' exercise of the rights granted herein. X X 7. The Free Software Foundation may publish revised and/or new versions Xof the General Public License from time to time. Such new versions will Xbe similar in spirit to the present version, but may differ in detail to Xaddress new problems or concerns. X XEach version is given a distinguishing version number. If the Program Xspecifies a version number of the license which applies to it and "any Xlater version", you have the option of following the terms and conditions Xeither of that version or of any later version published by the Free XSoftware Foundation. If the Program does not specify a version number of Xthe license, you may choose any version ever published by the Free Software XFoundation. X X 8. If you wish to incorporate parts of the Program into other free Xprograms whose distribution conditions are different, write to the author Xto ask for permission. For software which is copyrighted by the Free XSoftware Foundation, write to the Free Software Foundation; we sometimes Xmake exceptions for this. Our decision will be guided by the two goals Xof preserving the free status of all derivatives of our free software and Xof promoting the sharing and reuse of software generally. X X NO WARRANTY X X 9. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY XFOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN XOTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES XPROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED XOR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF XMERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS XTO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE XPROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, XREPAIR OR CORRECTION. X X 10. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING XWILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR XREDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, XINCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING XOUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED XTO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY XYOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER XPROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE XPOSSIBILITY OF SUCH DAMAGES. X X END OF TERMS AND CONDITIONS X X Appendix: How to Apply These Terms to Your New Programs X X If you develop a new program, and you want it to be of the greatest Xpossible use to humanity, the best way to achieve this is to make it Xfree software which everyone can redistribute and change under these Xterms. X X To do so, attach the following notices to the program. It is safest to Xattach them to the start of each source file to most effectively convey Xthe exclusion of warranty; and each file should have at least the X"copyright" line and a pointer to where the full notice is found. X X X Copyright (C) 19yy X X This program is free software; you can redistribute it and/or modify X it under the terms of the GNU General Public License as published by X the Free Software Foundation; either version 1, or (at your option) X any later version. X X This program is distributed in the hope that it will be useful, X but WITHOUT ANY WARRANTY; without even the implied warranty of X MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X GNU General Public License for more details. X X You should have received a copy of the GNU General Public License X along with this program; if not, write to the Free Software X Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X XAlso add information on how to contact you by electronic and paper mail. X XIf the program is interactive, make it output a short notice like this Xwhen it starts in an interactive mode: X X Gnomovision version 69, Copyright (C) 19xx name of author X Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. X This is free software, and you are welcome to redistribute it X under certain conditions; type `show c' for details. X XThe hypothetical commands `show w' and `show c' should show the Xappropriate parts of the General Public License. Of course, the Xcommands you use may be called something other than `show w' and `show Xc'; they could even be mouse-clicks or menu items--whatever suits your Xprogram. X XYou should also get your employer (if you work as a programmer) or your Xschool, if any, to sign a "copyright disclaimer" for the program, if Xnecessary. Here a sample; alter the names: X X Yoyodyne, Inc., hereby disclaims all copyright interest in the X program `Gnomovision' (a program to direct compilers to make passes X at assemblers) written by James Hacker. X X , 1 April 1989 X Ty Coon, President of Vice X XThat's all there is to it! END_OF_FILE if test 12488 -ne `wc -c <'ProSearch2.0/COPYING'`; then echo shar: \"'ProSearch2.0/COPYING'\" unpacked with wrong size! fi # end of 'ProSearch2.0/COPYING' fi if test -f 'ProSearch2.0/INSTALL' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/INSTALL'\" else echo shar: Extracting \"'ProSearch2.0/INSTALL'\" \(1668 characters\) sed "s/^X//" >'ProSearch2.0/INSTALL' <<'END_OF_FILE' XINSTALLATION for UNIX(tm) Systems X X1) Get the Prosite Database from your nearest molecular biology server X (e.g. ftp to ncbi.nlm.nih.gov, cd to repository/prosite and X get all the files there). X X Place these files in a directory hereafter refered to as PROSITE. X Generally, I place all the ProSite stuff in the same directory as X this code. X X2) If you do not have a working version of Awk conforming to the X specifications for new awk (nawk) get one from a arever near you. X The fastest awk I know of is mawk and is available many places X including "server.uga.edu" /usr/pub/packages/mawk.1.1.tar.Z X Place the compiled version of awk in a general place in your path. X Awk is a very useful langauge for small projects. Place the X awk executable in your path. X X3) Get readseq (a general sequence format translator, and can be X obtained from ftp.bio.indiana.edu. This code requires an ANSI X C compiler but compiled versions for some systems are available. X Follow the instructions for Readseq to install that program in X your path. X X4) Edit the Makefile to define locations to find PROSITE and these X files refered to as PROSEARCH as well as AWK. X X5) Type make to generate the regex file and executable shell scripts. X If your computers C compiler is not ansi compatible, type 'make sun' X instead. X X6) Type 'make test'. If there are errors or if a file called prosite.error X is generated you may have to fiddle around a little with the shell X scripts. X X7) Type 'make install' to get rid of unnecessary files. X X8) Move the file 'prosearch' to a place in the path. X X X X$Id: INSTALL,v 1.4 1992/04/09 02:09:57 lfk Exp $END_OF_FILE END_OF_FILE if test 1668 -ne `wc -c <'ProSearch2.0/INSTALL'`; then echo shar: \"'ProSearch2.0/INSTALL'\" unpacked with wrong size! fi # end of 'ProSearch2.0/INSTALL' fi if test -f 'ProSearch2.0/Makefile' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/Makefile'\" else echo shar: Extracting \"'ProSearch2.0/Makefile'\" \(1330 characters\) sed "s/^X//" >'ProSearch2.0/Makefile' <<'END_OF_FILE' X# Makefile for ProSearch X# $Id: Makefile,v 1.4 1992/04/09 02:09:57 lfk Exp $ X X# EDIT HERE X# define these variables to be where the database and the X# searching tools will be stored, ideally the same X XPROSITE=/usr/people/khorana/lfk/ProSearch XPROSEARCH=/usr/people/khorana/lfk/ProSearch X X# define the name of the implementation of awk you use XAWK=mawk X X# You should not need to edit below here X X# targets Xall: prosearch regex_update cregexa prosite.regex Xsun: prosearch regex_update cregexkr prosite.regex Xhelp: prosearch.help X Xcregexa: cregex_ansi.o X $(CC) -O cregex_ansi.o -o cregex X Xcregexkr: cregex_sun.o X $(CC) -O cregex_sun.o -o cregex X Xprosite.regex: prosite.dat X -regex_update X Xprosearch: prosearch.orig X @cat prosearch.orig | \ X sed 's^@PROSITE@^$(PROSITE)^g' | \ X sed 's^@PROSEARCH@^$(PROSEARCH)^g' | \ X sed 's^@AWK@^$(AWK)^g' > prosearch X chmod +x prosearch X Xregex_update: regex_update.orig X @cat regex_update.orig | \ X sed 's^@PROSITE@^$(PROSITE)^g' > regex_update X chmod +x regex_update X Xprosearch.help: prosearch.1 X groff -Tascii -man prosearch.1 > prosearch.help X Xtest: X ./prosearch -d -s test.pep > test.prosearch X @diff test.prosearch test.out X @echo There should be no errors X Xclean: X rm -f regex_update prosearch cregex *.o prosite.regex X Xinstall: X compress prosite.dat X rm *.orig *.c INSTALL *.o rm test* END_OF_FILE if test 1330 -ne `wc -c <'ProSearch2.0/Makefile'`; then echo shar: \"'ProSearch2.0/Makefile'\" unpacked with wrong size! fi # end of 'ProSearch2.0/Makefile' fi if test -f 'ProSearch2.0/README' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/README'\" else echo shar: Extracting \"'ProSearch2.0/README'\" \(3800 characters\) sed "s/^X//" >'ProSearch2.0/README' <<'END_OF_FILE' XINTRODUCTION X X Over the past year or so Amos Bairoch (bairoch X@cgecmu51.BITNET) has released an number of versions of his Prosite Xdatabase. This is a database of patterns which have been associated Xwith particular enzymatic activities or structures. For example, the Xwell known pattern for N-link glycosylation Asn-Xxx-Ser/Thr. X X Amos has compiled a database that consists of references about Xeach pattern, validity of the patterns, occurrences, and a host of Xother details. This database is of general use, and has been used by XAmos in his PC/Gene Suite of programs for analysis of DNA and Protein Xsequences. X X I wanted to use this database on a Unix machine and be able to Xask the question, "Which of these patterns occur in sequence X?" X X This is the second release of Prosearch. It completely Xsupersedes the first version with one important bug fix, and support Xfor VMS, MS-DOS, and UNIX. Also, by using ReadSeq, a fine program Xfrom Don Gilbert , more protein Xdata formats are accessible. X XIMPLEMENTATION X X Most patterns can be expressed as regular expressions. For Xexample the pattern '^P' when used with the unix utility grep matches Xany line in the input that begins with a 'P'. X X I translated all but 1 of the 337 patterns in Prosite to Unix Xstyle regular expressions and wrote a simple searching program to Xsearch a protein sequence for their occurrence. The pattern I did not Xtranslate was the pattern PS0003 which is Tyrosine Sulfation. There is Xno clean pattern for this modification. X X The program is written in the Awk language, and runs on Xmachines which have either Nawk from AT&T, Gawk from the Free Software XFoundation, or one of several versions of Awk which run on MSDOS Xcompatibles. Read the approriate INSTALL file for details. X XINPUT FILES X X In put file are any protein sequence files in an unstructured Xformat. AWK will accept the input on any number of lines of any length X(I've tried proteins sequences up to 2500 amino acids on one line with Xno problem). Each ASCII character will be interpreted as an amino Xacid, and all letters must be capitalized. With 'readseq' any of a Xnumber of formats can be used. X XOUTPUT X X There are two possible forms of output. The "short" form is a Xtable of accession numbers, positions in the sequence and short names Xfor patterns. The "long" form is the same except that the relevant Xsections from the Prosite Database is also printed. X XHere is an example of the short output for Bovine Rhodopsin. X XProsite Database -- Release 5.0 of April 1990 Copyright: Amos Bairoch XProSearch Software -- Release 0.1beta -- Copyright: Lee Kolakowski XThe following patterns are in < test.ops >: X XAccess# From->To Name X_______ ________ ____ XPS00001 2->6 ASN_GLYCOSYLATION XPS00001 15->19 ASN_GLYCOSYLATION XPS00001 200->204 ASN_GLYCOSYLATION XPS00005 14->17 PKC_PHOSPHO_SITE XPS00005 229->232 PKC_PHOSPHO_SITE XPS00005 243->246 PKC_PHOSPHO_SITE XPS00006 22->26 CK2_PHOSPHO_SITE XPS00006 193->197 CK2_PHOSPHO_SITE XPS00006 198->202 CK2_PHOSPHO_SITE XPS00006 229->233 CK2_PHOSPHO_SITE XPS00006 338->342 CK2_PHOSPHO_SITE XPS00007 21->30 TYR_PHOSPHO_SITE XPS00008 89->95 MYRISTYL XPS00008 120->126 MYRISTYL XPS00008 156->162 MYRISTYL XPS00008 182->188 MYRISTYL XPS00013 157->168 PROKAR_LIPOPROTEIN XPS00237 68->85 G_PROTEIN_RECEPTOR XPS00238 296->314 OPSIN X XUSAGE X X This is described in the file pros.1, a printable version is Xin pros.nro. X X XBUGS X X Please send bug reports or improvements to me. X XNOTICES X X This code is covered by the Free Software Foundation's Gnu XPublic License. See the file COPYING for details. X X XFrank Kolakowski X$Id: README,v 1.2 1992/04/08 22:56:25 lfk Exp $ END_OF_FILE if test 3800 -ne `wc -c <'ProSearch2.0/README'`; then echo shar: \"'ProSearch2.0/README'\" unpacked with wrong size! fi # end of 'ProSearch2.0/README' fi if test -f 'ProSearch2.0/cregex_ansi.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/cregex_ansi.c'\" else echo shar: Extracting \"'ProSearch2.0/cregex_ansi.c'\" \(13050 characters\) sed "s/^X//" >'ProSearch2.0/cregex_ansi.c' <<'END_OF_FILE' X/* This is distributed with Prosearch with the permission of X the author. */ X/* $Id: cregex_ansi.c,v 1.2 1992/04/08 22:56:25 lfk Exp $ */ X/*** program cregex *********************************************************** X * X * X * Name: X * cregex : create regex-file from PROSITE for use with PROSEARH. X * X * X * Syntax: X * cregex X * X * X * Description: X * Cregex creates the file containing valid AWK regular expressions, X * from the native PROSITE data bank. This file is used in Kolakowski's X * PROSEARCH script. X * For appearances, the output-file may be sorted alphabetically. X * X * X * Author: X * Jack A.M. Leunissen, CAOS/CAMM Center, Nijmegen, The Netherlands. X * X * X * Version: Date: By: Update: X * 1.0 23-Oct-1990 JackL - X * 1.01 26-Nov-1990 JackL Bug in check_title() fixed. X * 1.1 26-Dec-1990 JackL Processing changed. X * X */ X X/*** preprocessor ************************************************************* X * X */ X X#include X#include X#include X X#define MAXLEN 512 X#define MAXNUM 100 X#define MAXSTR 512 X#define MAXWRD 30 X#define MAXCOD 10 X#define MAXTTL 80 X#define MAXDOC 10 X X#define TRUE 1 X#define FALSE 0 X X#define N_TERM 1 X#define C_TERM 2 X#define INLIST 4 X#define EXCLUD 8 X X#define NEWLINE '\012' X X/*** globals ****************************************************************** X * X */ X Xchar pattern[MAXNUM][MAXLEN], word[MAXWRD], *ptr; Xchar code[MAXCOD], title[MAXTTL], patlin[MAXSTR], docu[MAXDOC]; Xint number; XFILE *fi, *fo; X X/*** prototypes *************************************************************** X * X */ X Xvoid open_files(int, char **); Xint read_data(void); Xvoid check_title(void); Xvoid extract(char *, char *, char); Xint get_pat(char *, char *, char); Xvoid initialize(void); Xint read_word(void); Xvoid process(void); Xvoid add_pattern(char *, int, int); Xvoid print_pat(void); Xint parse_word(char *, int *, int *); Xvoid close_files(void); X X/*** main ********************************************************************* X * X */ X Xint main(int argc, char **argv) X{ X int not_done; X X open_files(argc, argv); X while (read_data()) { X initialize(); X do { X not_done = read_word(); X process(); X } while (not_done); X print_pat(); X } X close_files(); X} X X/*** open_files *************************************************************** X * X * Open the input-file (PROSITE.DAT) and output-file (PROSITE.REGEX). X * X */ X Xvoid open_files(int argc, char **argv) X{ X if (argc != 3) { X fprintf(stderr, "Usage: %s database regex-file\n", argv[0]); X exit(0); X } X if ((fi = fopen(argv[1], "r")) == NULL) { X fprintf(stderr, "%s: cannot open %s\n", argv[0], argv[1]); X exit(1); X } X if ((fo = fopen(argv[2], "w")) == NULL) { X fprintf(stderr, "%s: cannot create %s\n", argv[0], argv[2]); X exit(2); X } X} X X/*** read_data **************************************************************** X * X * ID-line -> title X * AC-line -> code X * PA-line -> pattern X * DO-line -> documentation X * //-line -> end of entry X * X */ X Xint read_data(void) X{ X char c, line[MAXSTR]; X int has_pat, ac_found; X X has_pat = FALSE; X X do { X /* X * Find the ID-line X * X */ X if (fgets(line, MAXSTR, fi) == NULL) return(FALSE); X while (line[0] != 'I' && line[1] != 'D') { X if (fgets(line, MAXSTR, fi) == NULL) X return(FALSE); X } X extract(title, line, ';'); X check_title(); X X /* X * Find the other relevant lines X * X */ X if (fgets(line, MAXSTR, fi) == NULL) return(FALSE); X ac_found = FALSE; X while (line[0] != '/' && line[1] != '/') { X if (line[0] == 'A' && line[1] == 'C') { X if (ac_found) X fprintf(stderr, X "Too many AC-lines in %s\n",code); X else { X extract(code, line, ';'); X ac_found++; X } X } X if (line[0] == 'P' && line[1] == 'A') { X if (!get_pat(patlin, line, '.')) X return(FALSE); X has_pat++; X } X if (line[0] == 'D' && line[1] == 'O') X extract(docu, line, ';'); X if (fgets(line, MAXSTR, fi) == NULL) X return(FALSE); X } X } while (!has_pat); X X return(TRUE); X} X X/*** extract ****************************************************************** X * X * Extract a substring 'so' from string 'si', ending with character 'end'. X * X */ X Xvoid extract(char *so, char *si, char end) X{ X while (*si != ' ') *si++; /* skip code */ X while (*si == ' ') *si++; /* skip blanks */ X while (*si != end) *so++ = *si++; /* find end */ X *so = '\0'; X} X X/*** get_pat ****************************************************************** X * X * Extract the pattern from the PA-line(s). X * X */ X Xint get_pat(char *so, char *si, char end) X{ Xcont: X while (*si != ' ') *si++; /* skip code */ X while (*si == ' ') *si++; /* skip blanks */ X while (*si && *si != end && *si != NEWLINE) X *so++ = *si++; X if (*si != end) { X if (fgets(si, MAXSTR, fi) == NULL) return(FALSE); X goto cont; X } X *so++ = end; X *so = '\0'; X return(TRUE); X} X X/*** check_title ************************************************************** X * X * Check the title for the occurrence of blanks, and change them into X * underscores. X * NOTE: This function is obsolete! X * X */ X Xvoid check_title(void) X{ X char *s = title; X while (*s) { X *s = (*s == ' ') ? '_' : *s; X *s++; X } X} X X/*** close_files ************************************************************** X * X * Close the input- and output-file. X * X */ X Xvoid close_files(void) X{ X fclose(fi); X fclose(fo); X exit(0); X} X X/*** initialize *************************************************************** X * X * Initialize the pattern. X * X */ X Xvoid initialize(void) X{ X int i; X number = 1; X for (i = 0; i < MAXNUM; pattern[i++][0] = '\0'); X ptr = patlin; X} X X/*** read_word **************************************************************** X * X * Read a 'word', i.e. one pattern entity. X * X */ X Xint read_word(void) X{ X char *w = word; X X while (*ptr != '-' && *ptr != '.') { X *w++ = *ptr++; X } X *w = '\0'; X return ((int)*++ptr); X} X X/*** process ****************************************************************** X * X * Translate a pattern unit into valid AWK pattern description(s). X * X */ X Xvoid process(void) X{ X int first, last, numold, i, j, k, ret; X char str[MAXWRD], tmp[MAXSTR]; X X ret = parse_word(str, &first, &last); X X if (ret & N_TERM) { X /* X * Special case: N-terminus X */ X if (ret & INLIST && ! (ret & EXCLUD)) { X for (i = 0; i < number; i++) X strcpy(pattern[number+i], pattern[i]); X for (i = 0; i < number; i++) X strcat(pattern[i], "^"); X for (i = number; i < 2*number; i++) X strcat(pattern[i], str); X number *= 2; X } X else { X tmp[0] = (ret & EXCLUD) ? '.' : '^'; X tmp[1] = '\0'; X for (i = 0; i < number; i++) X strcat(pattern[i], tmp); X add_pattern(str, first, last); X } X } X X else if (ret & C_TERM) { X /* X * Special case: C-terminus X */ X if (ret & INLIST && ! (ret & EXCLUD)) { X for (i = 0; i < number; i++) X strcpy(pattern[number+i], pattern[i]); X for (i = 0; i < number; i++) X strcat(pattern[i], "$"); X for (i = number; i < 2*number; i++) X strcat(pattern[i], str); X number *= 2; X } X else { X add_pattern(str, first, last); X tmp[0] = (ret & EXCLUD) ? '.' : '$'; X tmp[1] = '\0'; X for (i = 0; i < number; i++) X strcat(pattern[i], tmp); X } X } X X else X /* X * No special case. X */ X add_pattern(str, first, last); X X X} X X/*** add_pattern ************************************************************** X * X */ X Xvoid add_pattern(char *str, int first, int last) X{ X int numold, i, j, k; X char tmp[MAXSTR]; X X numold = number; X if (last - first) { X for (i = first; i < last; i++) { X for (j = 0; j <= numold; j++) X strcpy(pattern[number+j], pattern[j]); X number += numold; X } X } X for (i = first; i <= last; i++) { X tmp[0] = '\0'; X for (j = 0; j < i; j++) X strcat(tmp, str); X for (j = 0; j < numold; j++) { X k = numold * (i - first) + j; X strcat(pattern[k], tmp); X } X } X} X X/*** parse_word *************************************************************** X * X * Parse the pattern entity: translate the 'word' into AWK rules, and X * determine the repeat factor/range, if present. X * X */ X Xint parse_word(char *str, int *first, int *last) X{ X char *w = word, *s = str; X int term, beg_list, end_list, exclude; X X *first = *last = 1; X term = beg_list = end_list = exclude = FALSE; X X do { X switch (*w) { X X case '<': X term |= N_TERM; X if (beg_list) X term |= INLIST; X break; X case '>': X term |= C_TERM; X if (beg_list && !end_list) X term |= INLIST; X break; X case 'x': X *s++ = '.'; X break; X case '[': X *s++ = '['; X beg_list = TRUE; X break; X case '{': X *s++ = '['; X *s++ = '^'; X exclude = EXCLUD; X beg_list = TRUE; X break; X case ']': X *s++ = ']'; X end_list = TRUE; X break; X case '}': X *s++ = ']'; X exclude = EXCLUD; X end_list = TRUE; X break; X case '(': X *first = *last = 0; X while (*++w != ',' && *w != ')') X *first = *first * 10 + *w - '0'; X if (*w == ',') X while (*++w != ',' && *w != ')') X *last = *last * 10 + *w - '0'; X else *last = *first; X break; X default: X *s++ = *w; X break; X } X } while (*w++); X X return (term|exclude); X} X X/*** print_pat **************************************************************** X * X * Store the translated pattern(s). X * X */ X Xvoid print_pat(void) X{ X int i; X X for (i = 0; i < number; i++) { X fprintf(fo, "%s ", code); X fprintf(fo, "%s ", pattern[i]); X fprintf(fo, "%s ", title); X fprintf(fo, "%s\n", docu); X } X} X X END_OF_FILE if test 13050 -ne `wc -c <'ProSearch2.0/cregex_ansi.c'`; then echo shar: \"'ProSearch2.0/cregex_ansi.c'\" unpacked with wrong size! fi # end of 'ProSearch2.0/cregex_ansi.c' fi if test -f 'ProSearch2.0/cregex_sun.c' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/cregex_sun.c'\" else echo shar: Extracting \"'ProSearch2.0/cregex_sun.c'\" \(13513 characters\) sed "s/^X//" >'ProSearch2.0/cregex_sun.c' <<'END_OF_FILE' X/* cregex is distributed with prosearch with the permission of the author */ X/* Modified for K&R compiler by XFrom reisner@ee.su.OZ.AU Fri Jan 18 12:25:20 1991 XSubject: cregex XFrank, X Again thanks for sending down the latest version of cregex. XAlec Dunn here at El. Eng. has modified it so that the standard C Xcompiler on the Sun won't complain. I'm taking the liberty of sending Xthe source to you (I also sent a copy to Amos Bairoch in case he might Xfind it of some use. Cheers,alex X*/ X/* $Id: cregex_sun.c,v 1.2 1992/04/08 22:56:25 lfk Exp $ */ X*** program cregex *********************************************************** X * Name: cregex : create regex-file from PROSITE for use with PROSEARH. X * Syntax: cregex X * Description: X * Cregex creates the file containing valid AWK regular expressions, X * from the native PROSITE data bank. This file is used in Kolakowski's X * PROSEARCH script. X * For appearances, the output-file may be sorted alphabetically. X * Author: X * Jack A.M. Leunissen, CAOS/CAMM Center, Nijmegen, The Netherlands. X * X * X * Version: Date: By: Update: X * 1.0 23-Oct-1990 JackL - X * 1.01 26-Nov-1990 JackL Bug in check_title() fixed. X * 1.1 26-Dec-1990 JackL Processing changed. X * X * Modified A Dunn, Jan 91, to remove ANSI-C features to allow X * compilation by Sun C compiler. Also closed the "preprocessor" X * comment below. X */ X X/*** preprocessor ************************************************************* X */ X X#include X#include X#include X X#define MAXLEN 512 X#define MAXNUM 100 X#define MAXSTR 512 X#define MAXWRD 30 X#define MAXCOD 10 X#define MAXTTL 80 X#define MAXDOC 10 X X#define TRUE 1 X#define FALSE 0 X X#define N_TERM 1 X#define C_TERM 2 X#define INLIST 4 X#define EXCLUD 8 X X#define NEWLINE '\012' X X/*** globals ****************************************************************** X * X */ X Xchar pattern[MAXNUM][MAXLEN], word[MAXWRD], *ptr; Xchar code[MAXCOD], title[MAXTTL], patlin[MAXSTR], docu[MAXDOC]; Xint number; XFILE *fi, *fo; X X/*** prototypes *************************************************************** X * X */ X Xvoid open_files(); Xint read_data(); Xvoid check_title(); Xvoid extract(); Xint get_pat(); Xvoid initialize(); Xint read_word(); Xvoid process(); Xvoid add_pattern(); Xvoid print_pat(); Xint parse_word(); Xvoid close_files(); X X/*** main ********************************************************************* X * X */ X Xint main(argc, argv) Xint argc; Xchar **argv; X{ X int not_done; X X open_files(argc, argv); X while (read_data()) { X initialize(); X do { X not_done = read_word(); X process(); X } while (not_done); X print_pat(); X } X close_files(); X} X X/*** open_files *************************************************************** X * X * Open the input-file (PROSITE.DAT) and output-file (PROSITE.REGEX). X * X */ X Xvoid open_files(argc, argv) Xint argc; Xchar **argv; X{ X if (argc != 3) { X fprintf(stderr, "Usage: %s database regex-file\n", argv[0]); X exit(0); X } X if ((fi = fopen(argv[1], "r")) == NULL) { X fprintf(stderr, "%s: cannot open %s\n", argv[0], argv[1]); X exit(1); X } X if ((fo = fopen(argv[2], "w")) == NULL) { X fprintf(stderr, "%s: cannot create %s\n", argv[0], argv[2]); X exit(2); X } X} X X/*** read_data **************************************************************** X * X * ID-line -> title X * AC-line -> code X * PA-line -> pattern X * DO-line -> documentation X * //-line -> end of entry X * X */ X Xint read_data() X{ X char c, line[MAXSTR]; X int has_pat, ac_found; X X has_pat = FALSE; X X do { X /* X * Find the ID-line X * X */ X if (fgets(line, MAXSTR, fi) == NULL) return(FALSE); X while (line[0] != 'I' && line[1] != 'D') { X if (fgets(line, MAXSTR, fi) == NULL) X return(FALSE); X } X extract(title, line, ';'); X check_title(); X X /* X * Find the other relevant lines X * X */ X if (fgets(line, MAXSTR, fi) == NULL) return(FALSE); X ac_found = FALSE; X while (line[0] != '/' && line[1] != '/') { X if (line[0] == 'A' && line[1] == 'C') { X if (ac_found) X fprintf(stderr, X "Too many AC-lines in %s\n",code); X else { X extract(code, line, ';'); X ac_found++; X } X } X if (line[0] == 'P' && line[1] == 'A') { X if (!get_pat(patlin, line, '.')) X return(FALSE); X has_pat++; X } X if (line[0] == 'D' && line[1] == 'O') X extract(docu, line, ';'); X if (fgets(line, MAXSTR, fi) == NULL) X return(FALSE); X } X } while (!has_pat); X X return(TRUE); X} X X/*** extract ****************************************************************** X * X * Extract a substring 'so' from string 'si', ending with character 'end'. X * X */ X Xvoid extract(so, si, end) Xchar *so; Xchar *si; Xchar end; X{ X while (*si != ' ') *si++; /* skip code */ X while (*si == ' ') *si++; /* skip blanks */ X while (*si != end) *so++ = *si++; /* find end */ X *so = '\0'; X} X X/*** get_pat ****************************************************************** X * X * Extract the pattern from the PA-line(s). X * X */ X Xint get_pat(so, si, end) Xchar *so; Xchar *si; Xchar end; X{ Xcont: X while (*si != ' ') *si++; /* skip code */ X while (*si == ' ') *si++; /* skip blanks */ X while (*si && *si != end && *si != NEWLINE) X *so++ = *si++; X if (*si != end) { X if (fgets(si, MAXSTR, fi) == NULL) return(FALSE); X goto cont; X } X *so++ = end; X *so = '\0'; X return(TRUE); X} X X/*** check_title ************************************************************** X * X * Check the title for the occurrence of blanks, and change them into X * underscores. X * NOTE: This function is obsolete! X * X */ X Xvoid check_title() X{ X char *s = title; X while (*s) { X *s = (*s == ' ') ? '_' : *s; X *s++; X } X} X X/*** close_files ************************************************************** X * X * Close the input- and output-file. X * X */ X Xvoid close_files() X{ X fclose(fi); X fclose(fo); X exit(0); X} X X/*** initialize *************************************************************** X * X * Initialize the pattern. X * X */ X Xvoid initialize() X{ X int i; X number = 1; X for (i = 0; i < MAXNUM; pattern[i++][0] = '\0'); X ptr = patlin; X} X X/*** read_word **************************************************************** X * X * Read a 'word', i.e. one pattern entity. X * X */ X Xint read_word() X{ X char *w = word; X X while (*ptr != '-' && *ptr != '.') { X *w++ = *ptr++; X } X *w = '\0'; X return ((int)*++ptr); X} X X/*** process ****************************************************************** X * X * Translate a pattern unit into valid AWK pattern description(s). X * X */ X Xvoid process() X{ X int first, last, numold, i, j, k, ret; X char str[MAXWRD], tmp[MAXSTR]; X X ret = parse_word(str, &first, &last); X X if (ret & N_TERM) { X /* X * Special case: N-terminus X */ X if (ret & INLIST && ! (ret & EXCLUD)) { X for (i = 0; i < number; i++) X strcpy(pattern[number+i], pattern[i]); X for (i = 0; i < number; i++) X strcat(pattern[i], "^"); X for (i = number; i < 2*number; i++) X strcat(pattern[i], str); X number *= 2; X } X else { X tmp[0] = (ret & EXCLUD) ? '.' : '^'; X tmp[1] = '\0'; X for (i = 0; i < number; i++) X strcat(pattern[i], tmp); X add_pattern(str, first, last); X } X } X X else if (ret & C_TERM) { X /* X * Special case: C-terminus X */ X if (ret & INLIST && ! (ret & EXCLUD)) { X for (i = 0; i < number; i++) X strcpy(pattern[number+i], pattern[i]); X for (i = 0; i < number; i++) X strcat(pattern[i], "$"); X for (i = number; i < 2*number; i++) X strcat(pattern[i], str); X number *= 2; X } X else { X add_pattern(str, first, last); X tmp[0] = (ret & EXCLUD) ? '.' : '$'; X tmp[1] = '\0'; X for (i = 0; i < number; i++) X strcat(pattern[i], tmp); X } X } X X else X /* X * No special case. X */ X add_pattern(str, first, last); X X X} X X/*** add_pattern ************************************************************** X * X */ X Xvoid add_pattern(str, first, last) Xchar *str; Xint first; Xint last; X{ X int numold, i, j, k; X char tmp[MAXSTR]; X X numold = number; X if (last - first) { X for (i = first; i < last; i++) { X for (j = 0; j <= numold; j++) X strcpy(pattern[number+j], pattern[j]); X number += numold; X } X } X for (i = first; i <= last; i++) { X tmp[0] = '\0'; X for (j = 0; j < i; j++) X strcat(tmp, str); X for (j = 0; j < numold; j++) { X k = numold * (i - first) + j; X strcat(pattern[k], tmp); X } X } X} X X/*** parse_word *************************************************************** X * X * Parse the pattern entity: translate the 'word' into AWK rules, and X * determine the repeat factor/range, if present. X * X */ X Xint parse_word(str, first, last) Xchar *str; Xint *first; Xint *last; X{ X char *w = word, *s = str; X int term, beg_list, end_list, exclude; X X *first = *last = 1; X term = beg_list = end_list = exclude = FALSE; X X do { X switch (*w) { X X case '<': X term |= N_TERM; X if (beg_list) X term |= INLIST; X break; X case '>': X term |= C_TERM; X if (beg_list && !end_list) X term |= INLIST; X break; X case 'x': X *s++ = '.'; X break; X case '[': X *s++ = '['; X beg_list = TRUE; X break; X case '{': X *s++ = '['; X *s++ = '^'; X exclude = EXCLUD; X beg_list = TRUE; X break; X case ']': X *s++ = ']'; X end_list = TRUE; X break; X case '}': X *s++ = ']'; X exclude = EXCLUD; X end_list = TRUE; X break; X case '(': X *first = *last = 0; X while (*++w != ',' && *w != ')') X *first = *first * 10 + *w - '0'; X if (*w == ',') X while (*++w != ',' && *w != ')') X *last = *last * 10 + *w - '0'; X else *last = *first; X break; X default: X *s++ = *w; X break; X } X } while (*w++); X X return (term|exclude); X} X X/*** print_pat **************************************************************** X * X * Store the translated pattern(s). X * X */ X Xvoid print_pat() X{ X int i; X X for (i = 0; i < number; i++) { X fprintf(fo, "%s ", code); X fprintf(fo, "%s ", pattern[i]); X fprintf(fo, "%s ", title); X fprintf(fo, "%s\n", docu); X } X} X X X X X X END_OF_FILE if test 13513 -ne `wc -c <'ProSearch2.0/cregex_sun.c'`; then echo shar: \"'ProSearch2.0/cregex_sun.c'\" unpacked with wrong size! fi # end of 'ProSearch2.0/cregex_sun.c' fi if test -f 'ProSearch2.0/prodoc.awk' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/prodoc.awk'\" else echo shar: Extracting \"'ProSearch2.0/prodoc.awk'\" \(2098 characters\) sed "s/^X//" >'ProSearch2.0/prodoc.awk' <<'END_OF_FILE' X# Written by X# Lee F. Kolakowski, Jr. X# Massachusetts General Hospital X# Endocrine Unit X# Wellman 5 X# Fruit Street X# Boston, MA 02114 X# X# COPYRIGHT X# Copyright (c) 1990, 1991, 1992 X# by Lee F. Kolakowski, Jr. All rights reserved. X# X# This program is free software; you can redistribute it and/or X# modify it under the terms of the GNU General Public License X# (version 1), as published by the Free Software Foundation, and X# found in the file 'COPYING' included with this distribution. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warrant of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# Send bugs or improvements to kolakowski@helix.mgh.harvard.edu X# X## X# This file is prodoc.awk. X# This code presents the results from the search perfomed by X# prosite.awk and is the interface to prosite.doc X# $Id: prodoc.awk,v 1.2 1992/04/08 22:56:25 lfk Exp $ X############################################################# X XBEGIN { X printf("\n%s\t%12s\t%20s\t%s\n", "Access#", "From->To", "Name", "Documetation#") X printf("%s\t%12s\t%20s\t%s\n", "_______", "________", "____", "_____________") X n=1 X count=1 X} X{ X if ($0 ~ /^PS/ && NF == 4) { X printf("%s\t%12s\t%20s\t%s\n", $1, $2, $3, $4) X regex[count] = "{"$4 X regex_num = count X count++ X } X else if ($0 ~ /^SITE/) { X gsub(/^SITE/, ""); print X } X else if ($0 ~ /^{PDOC/ && n < regex_num) { X for (i=n; i <= regex_num; i++) { X if ( regex[i] != regex_last ) { X regex_last = regex[i] X if (verbose) X print "regex ="regex[i], "line ="$0 X if (match($0,regex[i])) { X n = i X print $0 X while ( $0 !~ /{END}/) { X getline X print $0 X } X } X } X } X } X} END_OF_FILE if test 2098 -ne `wc -c <'ProSearch2.0/prodoc.awk'`; then echo shar: \"'ProSearch2.0/prodoc.awk'\" unpacked with wrong size! fi # end of 'ProSearch2.0/prodoc.awk' fi if test -f 'ProSearch2.0/prosearch.1' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/prosearch.1'\" else echo shar: Extracting \"'ProSearch2.0/prosearch.1'\" \(2248 characters\) sed "s/^X//" >'ProSearch2.0/prosearch.1' <<'END_OF_FILE' X.\" $Id: prosearch.1,v 1.2 1992/04/08 22:56:25 lfk Exp $ X.TH PROSEARCH 1 "Apr 8 1992" X.SH NAME Xprosearch \- search protein sequences for Prosite Database patterns X.SH SYNOPSIS X.B prosearch X[-sdh] [-rfilename] file ... X.br X.SH DESCRIPTION X.I prosearch Xreads each X.I file Xin sequence and searchs the contents for regular expression patterns Xdescribed in the Prosite Database. The output is displayed on the Xstandard output. ProSearch is written in the Awk programming language. X.LP XIf a pattern is found in a protein sequence, it does not necessarily Xmean that any structure or function attributed to that pattern is a Xcharacteristic of that protein. X.SH OPTIONS XThe following options added additional information to the output. X.TP 15 X.B \-s(ites) XIf the X.B \-s(ites) Xoption is specified, the amino acid sequence in the target protein Xand the regular expression are displayed. X.TP 15 X.B \-d(oc) XIf the X.B \-d(oc) Xoption is specified, the relevant information in the ProSite documentation Xis displayed for each pattern matched. X.TP 15 X.B \-rfilename XIf the X.B \-rfilename Xoption is specified, the argument should be a filename preceeded by -r with Xlocal patterns conforming to the following format on each line: X.sp Xaccession#patternnamedocumentation# X.sp XThe patterns must conform to the specifications of regular expressions in Xyour local version of Awk. X.LP XIf errors during processing occur, a file called "prosearch.error" will Xappear in your directory describing the error. X.SH SEE ALSO Xawk(1), gawk(1), nawk(1), or mawk(1) X.br Xcregex(1) translates prosite.dat to the regular expression format and Xwas written by Jack A.M. Leunissen, CAOS/CAMM Center, Nijmegen, The XNetherlands. X.br Xprosite.regex - the regular expression file X.br Xprosite.doc - the Prosite database (available from NETSERV@EMBL.BITNET) X.SH AUTHORS XProsearch was written by and is maintained by Lee F. Kolakowski, Jr. X(email lfk@eastman1.mit.edu). If a citation is need for ProSearch Xplease cite as "unpublished method." X.LP XThe ProSite Database is written and maintained by X.br XAmos Bairoch X.br XMedical Biochemistry Department X.br XUniversity of Geneva X.br XSwitzerland X.br XEmail: bairoch@cmu.unige.ch or bairoch@cgecmu51.bitnet X.br XTelephone: (+41 22) 618 492 X END_OF_FILE if test 2248 -ne `wc -c <'ProSearch2.0/prosearch.1'`; then echo shar: \"'ProSearch2.0/prosearch.1'\" unpacked with wrong size! fi # end of 'ProSearch2.0/prosearch.1' fi if test -f 'ProSearch2.0/prosearch.help' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/prosearch.help'\" else echo shar: Extracting \"'ProSearch2.0/prosearch.help'\" \(3187 characters\) sed "s/^X//" >'ProSearch2.0/prosearch.help' <<'END_OF_FILE' X X X XPROSEARCH(1) PROSEARCH(1) X X XNNAAMMEE X prosearch - search protein sequences for Prosite Database X patterns X XSSYYNNOOPPSSIISS X pprroosseeaarrcchh [-sdh] [-rfilename] file ... X XDDEESSCCRRIIPPTTIIOONN X _p_r_o_s_e_a_r_c_h reads each _f_i_l_e in sequence and searchs the con- X tents for regular expression patterns described in the X Prosite Database. The output is displayed on the standard X output. ProSearch is written in the Awk programming lan- X guage. X X If a pattern is found in a protein sequence, it does not X necessarily mean that any structure or function attributed X to that pattern is a characteristic of that protein. X XOOPPTTIIOONNSS X The following options added additional information to the X output. X X --ss((iitteess)) If the --ss((iitteess)) option is specified, the X amino acid sequence in the target protein X and the regular expression are displayed. X X --dd((oocc)) If the --dd((oocc)) option is specified, the rel- X evant information in the ProSite documenta- X tion is displayed for each pattern matched. X X --rrffiilleennaammee If the --rrffiilleennaammee option is specified, the X argument should be a filename preceeded by X -r with local patterns conforming to the X following format on each line: X X acces- X sion#patternnamedocumentation# X X The patterns must conform to the specifica- X tions of regular expressions in your local X version of Awk. X X If errors during processing occur, a file called "pros- X earch.error" will appear in your directory describing the X error. X XSSEEEE AALLSSOO X awk(1), gawk(1), nawk(1), or mawk(1) X cregex(1) translates prosite.dat to the regular expression X format and was written by Jack A.M. Leunissen, CAOS/CAMM X Center, Nijmegen, The Netherlands. X prosite.regex - the regular expression file X prosite.doc - the Prosite database (available from NET- X SERV@EMBL.BITNET) X X X X Apr 8 1992 1 X X X X X XPROSEARCH(1) PROSEARCH(1) X X XAAUUTTHHOORRSS X Prosearch was written by and is maintained by Lee F. X Kolakowski, Jr. (email lfk@eastman1.mit.edu). If a cita- X tion is need for ProSearch please cite as "unpublished X method." X X The ProSite Database is written and maintained by X Amos Bairoch X Medical Biochemistry Department X University of Geneva X Switzerland X Email: bairoch@cmu.unige.ch or bairoch@cgecmu51.bitnet X Telephone: (+41 22) 618 492 X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X Apr 8 1992 2 X X END_OF_FILE echo shar: 114 control characters may be missing from \"'ProSearch2.0/prosearch.help'\" if test 3187 -ne `wc -c <'ProSearch2.0/prosearch.help'`; then echo shar: \"'ProSearch2.0/prosearch.help'\" unpacked with wrong size! fi # end of 'ProSearch2.0/prosearch.help' fi if test -f 'ProSearch2.0/prosearch.orig' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/prosearch.orig'\" else echo shar: Extracting \"'ProSearch2.0/prosearch.orig'\" \(2366 characters\) sed "s/^X//" >'ProSearch2.0/prosearch.orig' <<'END_OF_FILE' X#!/bin/sh X X# Written by X# Lee F. Kolakowski, Jr. X# Massachusetts General Hospital X# Endocrine Unit X# Wellman 5 X# Fruit Street X# Boston, MA 02114 X# X# COPYRIGHT X# Copyright (c) 1990, 1991, 1992 X# by Lee F. Kolakowski, Jr. All rights reserved. X# X# This program is free software; you can redistribute it and/or X# modify it under the terms of the GNU General Public License X# (version 1), as published by the Free Software Foundation, and X# found in the file 'COPYING' included with this distribution. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warrant of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# Send bugs or improvements to kolakowski@helix.mgh.harvard.edu X# X# $Id: prosearch.orig,v 1.3 1992/04/08 23:42:04 lfk Exp $ X X Xtrap 'rm -f /tmp/pros$$.tmp' 0 X X# shell variables X#awk='nawk' #AT&T Awk X#awk='mawk' #fastest X#awk='gawk' #slowest Xawk=@AWK@ X Xversion=2.0 Xdb_version=8.1 X Xsite_dir='@PROSITE@' Xsearch_dir='@PROSEARCH@' X Xprosearch=${search_dir}/prosite.awk Xregsites=${site_dir}/prosite.regex Xdocumentation=${site_dir}/prosite.doc Xhelpfile=${search_dir}/prosearch.help Xdocflag="" Xsiteflag=no X X# process arguments Xfor arg in $* Xdo case $arg in X -s*) siteflag=yes ;; # display sites in output X -d*) docflag=${documentation} ;; # display documentation X -h*) cat ${helpfile}; exit 0 ;; X -r*) regsites=`echo $arg | sed 's@-r@@'` ; X echo `basename $0`: using $regsites for pattern file ;; X -*) echo `basename $0`: unknown flag $arg ; X echo Usage: prosearch [-sites] [-doc] -[help] -rfile filenames; X exit 1 ;; X *) args="${args} $arg" ;; # echo $args ;; X esac Xdone X Xecho "ProSearch${version} searches The Prosite Database ${db_version}" Xfor file in $args Xdo X echo "The following ProSite Patterns are in < $file >:" X readseq -C -f13 -p < $file > /tmp/pros$$.tmp X ${awk} -f ${prosearch} -v showsites=$siteflag ${regsites} /tmp/pros$$.tmp | X ${awk} -f ${search_dir}/prodoc.awk - $docflag X rm -f /tmp/pros$$.tmp Xdone X END_OF_FILE if test 2366 -ne `wc -c <'ProSearch2.0/prosearch.orig'`; then echo shar: \"'ProSearch2.0/prosearch.orig'\" unpacked with wrong size! fi # end of 'ProSearch2.0/prosearch.orig' fi if test -f 'ProSearch2.0/prosite.awk' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/prosite.awk'\" else echo shar: Extracting \"'ProSearch2.0/prosite.awk'\" \(3495 characters\) sed "s/^X//" >'ProSearch2.0/prosite.awk' <<'END_OF_FILE' X# Written by X# Lee F. Kolakowski, Jr. X# Massachusetts General Hospital X# Endocrine Unit X# Wellman 5 X# Fruit Street X# Boston, MA 02114 X# X# This version was modified extensively by Joe Smith (jes@mbio.med.upenn.edu) X# X# COPYRIGHT X# Copyright (c) 1990, 1991, 1992 X# by Lee F. Kolakowski, Jr. All rights reserved. X# X# This program is free software; you can redistribute it and/or X# modify it under the terms of the GNU General Public License X# (version 1), as published by the Free Software Foundation, and X# found in the file 'COPYING' included with this distribution. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warrant of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# Send bugs or improvements to kolakowski@helix.mgh.harvard.edu X# X## X# This file is prosite.awk. X# This code searchs a target sequence for patterns in the regex format X# X# $Id: prosite.awk,v 1.2 1992/04/08 22:56:25 lfk Exp $ X############################################################# X XBEGIN { X# Increase to 11 for a file with debugging output "x.msg" X verbose = 0 X me = "prosite.awk" X errfile = msgfile = "prosite.error" X X if (ARGC < 2) { X printf "%s: missing pattern filename\n", me >errfile X exit 1 X } X npat = get_patterns( ARGV[1] ) X if (verbose) X printf "%s: %d patterns read from %s\n", me, npat, ARGV[1] >msgfile; X X if ( ARGC > 2 ) X for (i = 2; i < ARGC; ++i) X prosite( ARGV[i] ) X else if ( ARGC == 2 ) X prosite( "/dev/stdin" ) X exit X} X Xfunction get_patterns ( patfile, n) { X for (n = 0; getline < patfile; ++n) { X if (NF == 4) { X accession[n] = $1 ; X pattern[n] = $2; X name[n] = $3; X doc[n] = $4; X } X else { X printf "%s: error in pattern file '%s', line %d\n", X me, patfile, n+1 >errfile X exit 1 X } X } X close(patfile) X $0 = "" X return n X} X Xfunction prosite ( seqfile, i, offset, from, to, sites, matched) { X# read & build the sequence string X for (seq = $0; getline 0; seq = seq$0) X ; X if (verbose) X printf "%s: read %d aa from %s\n", X me, length(seq), seqfile >msgfile X if (verbose >= 10) X for (offset = 1; offset < length(seq); offset += 50) X print substr(seq, offset, 50) >msgfile; X X for (i = 0; i < npat; ++i) { X if (verbose >= 10) X printf "%s: searching for %s (%d of %d)\n", X me, accession[i], i+1, npat >msgfile X sites = 0 X offset = 1 X while (match(substr(seq, offset), pattern[i])) { X ++sites X from = offset + RSTART - 1 X to = from + RLENGTH - 1 X printf("%s\t%d->%d\t%s\t%s\n", X accession[i], from, to, name[i], doc[i]); X if (showsites == "YES" || showsites == "yes") X printf "SITE\tPattern\t%s matched\nSITE\tSite\t%d %s %d\n", X pattern[i], from, substr(seq, from, RLENGTH), to X if (verbose >= 10) X printf "%s: %s matched %s\n", me, pattern[i], X substr(seq, from, RLENGTH) >msgfile X offset = from + 1 X } X if (sites) X ++matched X allsites += sites X } X if (verbose) X printf "%s: %d patterns matched at %d sites\n", X me, matched, allsites >msgfile X} END_OF_FILE if test 3495 -ne `wc -c <'ProSearch2.0/prosite.awk'`; then echo shar: \"'ProSearch2.0/prosite.awk'\" unpacked with wrong size! fi # end of 'ProSearch2.0/prosite.awk' fi if test -f 'ProSearch2.0/regex_update.orig' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/regex_update.orig'\" else echo shar: Extracting \"'ProSearch2.0/regex_update.orig'\" \(1621 characters\) sed "s/^X//" >'ProSearch2.0/regex_update.orig' <<'END_OF_FILE' X#!/bin/sh X# X# Update the ProSearch regular expression file X# X# Written by X# Lee F. Kolakowski, Jr. X# Massachusetts General Hospital X# Endocrine Unit X# Wellman 5 X# Fruit Street X# Boston, MA 02114 X# X# COPYRIGHT X# Copyright (c) 1990, 1991, 1992 X# by Lee F. Kolakowski, Jr. All rights reserved. X# X# This program is free software; you can redistribute it and/or X# modify it under the terms of the GNU General Public License X# (version 1), as published by the Free Software Foundation, and X# found in the file 'COPYING' included with this distribution. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warrant of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# Send bugs or improvements to kolakowski@helix.mgh.harvard.edu X# X# $Id: regex_update.orig,v 1.2 1992/04/08 22:56:25 lfk Exp $ X Xsite_dir='@PROSITE@' XDATA=$site_dir/prosite.dat XREGEX=$site_dir/prosite.regex XCREGEX=cregex X X#if [ $DATA -nt $REGEX ]; then X# echo Updateing $REGEX with $DATA X# mv $REGEX ${REGEX}.old X# cregex $DATA $REGEX X# sort $REGEX -o $REGEX X#else X# echo $REGEX is up to date X#fi X Xecho -n Updating `basename $REGEX` with `basename $DATA` ... Xmv $REGEX ${REGEX}.old Xcregex $DATA $REGEX Xsort $REGEX -o $REGEX Xecho done END_OF_FILE if test 1621 -ne `wc -c <'ProSearch2.0/regex_update.orig'`; then echo shar: \"'ProSearch2.0/regex_update.orig'\" unpacked with wrong size! fi # end of 'ProSearch2.0/regex_update.orig' fi if test -f 'ProSearch2.0/test.out' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/test.out'\" else echo shar: Extracting \"'ProSearch2.0/test.out'\" \(15369 characters\) sed "s/^X//" >'ProSearch2.0/test.out' <<'END_OF_FILE' XProSearch2.0 searches The Prosite Database 8.1 XThe following ProSite Patterns are in < test.pep >: X XAccess# From->To Name Documetation# X_______ ________ ____ _____________ XPS00001 2->5 ASN_GLYCOSYLATION PDOC00001 X Pattern N[^P][ST][^P] matched X Site 2 NGTE 5 XPS00001 15->18 ASN_GLYCOSYLATION PDOC00001 X Pattern N[^P][ST][^P] matched X Site 15 NKTG 18 XPS00001 200->203 ASN_GLYCOSYLATION PDOC00001 X Pattern N[^P][ST][^P] matched X Site 200 NESF 203 XPS00005 14->16 PKC_PHOSPHO_SITE PDOC00005 X Pattern [ST].[RK] matched X Site 14 SNK 16 XPS00005 229->231 PKC_PHOSPHO_SITE PDOC00005 X Pattern [ST].[RK] matched X Site 229 TVK 231 XPS00005 243->245 PKC_PHOSPHO_SITE PDOC00005 X Pattern [ST].[RK] matched X Site 243 TQK 245 XPS00006 22->25 CK2_PHOSPHO_SITE PDOC00006 X Pattern [ST]..[DE] matched X Site 22 SPFE 25 XPS00006 193->196 CK2_PHOSPHO_SITE PDOC00006 X Pattern [ST]..[DE] matched X Site 193 TPHE 196 XPS00006 198->201 CK2_PHOSPHO_SITE PDOC00006 X Pattern [ST]..[DE] matched X Site 198 TNNE 201 XPS00006 229->232 CK2_PHOSPHO_SITE PDOC00006 X Pattern [ST]..[DE] matched X Site 229 TVKE 232 XPS00006 338->341 CK2_PHOSPHO_SITE PDOC00006 X Pattern [ST]..[DE] matched X Site 338 SKTE 341 XPS00007 21->29 TYR_PHOSPHO_SITE PDOC00007 X Pattern [RK]...[DE]...Y matched X Site 21 RSPFEAPQY 29 XPS00008 89->94 MYRISTYL PDOC00008 X Pattern G[^EDRKHPFYW]..[STAGCN][^P] matched X Site 89 GGFTTT 94 XPS00008 120->125 MYRISTYL PDOC00008 X Pattern G[^EDRKHPFYW]..[STAGCN][^P] matched X Site 120 GGEIAL 125 XPS00008 156->161 MYRISTYL PDOC00008 X Pattern G[^EDRKHPFYW]..[STAGCN][^P] matched X Site 156 GVAFTW 161 XPS00008 182->187 MYRISTYL PDOC00008 X Pattern G[^EDRKHPFYW]..[STAGCN][^P] matched X Site 182 GMQCSC 187 XPS00237 123->139 G_PROTEIN_RECEPTOR PDOC00210 X Pattern [GSTALIVMC][GSTAPDE][^EDPKRH]..[LIVMNG]..[LIVMFT][GSTAN][LIVMFYWAS][DEN]R[FYWCH]..[LIVM] matched X Site 123 IALWSLVVLAIERYVVV 139 XPS00238 296->313 OPSIN PDOC00211 X Pattern K.....[DN]P.[IV]Y......[FY] matched X Site 296 KTSAVYNPVIYIMMNKQF 313 X{PDOC00001} X{PS00001; ASN_GLYCOSYLATION} X{BEGIN} X************************ X* N-glycosylation site * X************************ X XIt has been known for a long time [1] that potential N-glycosylation sites are Xspecific to the consensus sequence Asn-Xaa-Ser/Thr. It must be noted that the Xpresence of the consensus tripeptide is not sufficient to conclude that an Xasparagine residue is glycosylated, due to the fact that the folding of the Xprotein plays an important role in the regulation of N-glycosylation [2]. It Xhas been shown [3] that the presence of proline between Asn and Ser/Thr will Xinhibit N-glycosylation; this has been confirmed by a recent [4] statistical Xanalysis of glycosylation sites, which also shows that about 50% of the sites Xthat have a proline C-terminal to Ser/Thr are not glycosylated. X XIt must also be noted that there are a few reported cases of glycosylation Xsites with the pattern Asn-Xaa-Cys; an experimentally demonstrated occurrence Xof such non-standard site is found in the plasma protein C [5]. X X-Consensus pattern: N-{P}-[ST]-{P} X [N is the glycosylation site] X-Last update: May 1991 / Text revised. X X[ 1] Marshall R.D. X Annu. Rev. Biochem. 41:673-702(1972). X[ 2] Pless D.D., Lennarz W.J. X Proc. Natl. Acad. Sci. U.S.A. 74:134-138(1977). X[ 3] Bause E. X Biochem. J. 209:331-336(1983). X[ 4] Gavel Y., von Heijne G. X Protein Eng. 3:433-442(1990). X[ 5] Miletich J.P., Broze G.J. Jr. X J. Biol. Chem. 265:11397-11404(1990). X{END} X{PDOC00005} X{PS00005; PKC_PHOSPHO_SITE} X{BEGIN} X***************************************** X* Protein kinase C phosphorylation site * X***************************************** X XIn vivo, protein kinase C exhibits a preference for the phosphorylation of Xserine or threonine residues close to a C-terminal basic residue [1,2]. The Xpresence of additional basic residues at the N- or C-terminal of the target Xamino acid enhances the Vmax and Km of the phosphorylation reaction. X X-Consensus pattern: [ST]-x-[RK] X [S or T is the phosphorylation site] X-Last update: June 1988 / First entry. X X[ 1] Woodget J.R., Gould K.L., Hunter T. X Eur. J. Biochem. 161:177-184(1986). X[ 2] Kishimoto A., Nishiyama K., Nakanishi H., Uratsuji Y., Nomura H., X Takeyama Y., Nishizuka Y. X J. Biol. Chem. 260:12492-12499(1985). X{END} X{PDOC00006} X{PS00006; CK2_PHOSPHO_SITE} X{BEGIN} X***************************************** X* Casein kinase II phosphorylation site * X***************************************** X XCasein kinase II (CK-2) is a protein serine/threonine kinase that has activity Xindependent of cyclic nucleotides and of calcium. CK-2 phosphorylates many Xdifferent proteins. The substrate specificity [1] of this enzyme can be Xsummarized as follows: X X (1) Under comparable conditions Ser is favoured over Thr. X (2) An acidic residue (either Asp or Glu) must be present three residues to X the C-terminal of the phosphate acceptor site. X (3) Additional acidic residues in positions +1, +2, +4, and +5 increase the X phosphorylation rate. Most physiological substrates have at least one X acidic residue in these positions. X (4) Asp is preferred to Glu as the provider of acidic determinants. X (5) A basic residue to the N-terminal of the acceptor site decreases the X phosphorylation rate, while an acidic one will increase it. X X-Consensus pattern: [ST]-x(2)-[DE] X [S or T is the phosphorylation site] X-Note: this pattern is found most, but not all, of the known physiological X substrates. X-Last update: May 1991 / Text revised. X X[ 1] Pinna L.A. X Biochim. Biophys. Acta 1054:267-284(1990). X{END} X{PDOC00007} X{PS00007; TYR_PHOSPHO_SITE} X{BEGIN} X**************************************** X* Tyrosine kinase phosphorylation site * X**************************************** X XSubstrates of tyrosine protein kinases are generally characterized by a lysine Xor an arginine seven residues to the N-terminal side of the phosphorylated Xtyrosine. An acidic residue (Asp or Glu) is often found at either three or Xfour residues to the N-terminal side of the tyrosine [1,2,3]. There are a Xnumber of exceptions to this rule such as the tyrosine phosphorylation sites Xof enolase and lipocortin II. X X-Consensus pattern: [RK]-x(2)-[DE]-x(3)-Y X or [RK]-x(3)-[DE]-x(2)-Y X [Y is the phosphorylation site] X-Last update: June 1988 / First entry. X X[ 1] Patschinsky T., Hunter T., Esch F.S., Cooper J.A., Sefton B.M. X Proc. Natl. Acad. Sci. U.S.A. 79:973-977(1982). X[ 2] Hunter T. X J. Biol. Chem. 257:4843-4848(1982). X[ 3] Cooper J.A., Esch F.S., Taylor S.S., Hunter T. X J. Biol. Chem. 259:7835-7841(1984). X{END} X{PDOC00008} X{PS00008; MYRISTYL} X{BEGIN} X************************* X* N-myristoylation site * X************************* X XAn appreciable number of eukaryotic proteins are acylated by the covalent Xaddition of myristate (a C14-saturated fatty acid) to their N-terminal residue Xvia an amide linkage [1,2]. The specificity of the enzyme responsible for Xthis modification, myristoyl CoA:protein N-myristoyl transferase (NMT), has Xbeen derived from the sequence of known N-myristoylated proteins and from Xstudies using synthetic peptides. The sequence specificity seems to be the Xfollowing: X X - The N-terminal residue must be glycine. X - In position 2, uncharged residues are allowed. Charged residues, proline X and large hydrophobic residues are not allowed. X - In positions 3 and 4, most, if not all, residues are allowed. X - In position 5, small uncharged residues are all allowed (Ala, Ser, Thr, X Cys, Asn and Gly). Serine is favored. X - In position 6, proline is not allowed. X X-Consensus pattern: G-{EDRKHPFYW}-x(2)-[STAGCN]-{P} X [G is the N-myristoylation site] X-Note: we deliberately include as potential myristoylated glycine residues X those which are internal to a sequence, for it could well be that the X sequence under study represents a viral polyprotein precursor and that X subsequent proteolytic processing could expose an internal glycine as the N- X terminal of a mature protein. X-Last update: October 1989 / Pattern and text revised. X X[ 1] Towler D.A., Gordon J.I., Adams S.P., Glaser L. X Annu. Rev. Biochem. 57:69-99(1988). X[ 2] Grand R.J.A. X Biochem. J. 258:625-638(1989). X{END} X{PDOC00210} X{PS00237; G_PROTEIN_RECEPTOR} X{BEGIN} X***************************************** X* G-protein coupled receptors signature * X***************************************** X XG-protein coupled receptors [1,2] (also called R7G) are an extensive group of Xhormones, neurotransmitters, and light receptors which transduce extracellular Xsignals by interaction with guanine nucleotide-binding (G) proteins. The Xreceptors that are currently known to belong to this family are listed below X(references are only provided for very recently sequenced proteins). X X - 5-hydroxytryptamine (serotonin) 1a, 1c and 2 [Reviewed in 3]. X - Acetylcholine, muscarinic-type, M1 to M5. X - Adenosine A1 and A2 [4]. X - Adrenergic alpha-1 and alpha-2; beta-1, beta-2, and beta-3 [Reviewed in 5]. X - Angiotensin II (proto-oncogene mas). X - Bombesin/gastrin-releasing peptide. X - C5a anaphylatoxin [6]. X - Cannabinoid. X - Dopamine D1 to D5 [Reviewed in 7]. X - Endothelin ETa and ETb [Reviewed in 8]. X - f-Met-Leu-Phe (fMLP) (N-formyl peptide). X - Follicle stimulating hormone (FSH-R) [Reviewed in 9]. X - Histamine H2 (gastric receptor I) [10]. X - Lutropin-choriogonadotropic hormone (LSH-R) [Reviewed in 9]. X - Neuromedin K (NK-3). X - Neurotensin. X - Octopamine, from insects. X - Odorants [11]. X - Platelet activating factor (PAF-R) [12]. X - Substance-K (NK-2). X - Substance-P (NK-1). X - Thromboxane A2 [13]. X - Thyrotropin (TSH-R) [Reviewed in 9]. X - Thyrotropin releasing factor. X - Visual pigments (opsins and rhodopsin) [Reviewed in 14]. X - Two putative receptors from dog: RDC1 and RDC4. X - Two putative receptors from rat: FC5, and RTA. X - Three putative receptors encoded in the genome of cytomegalovirus: US27, X US28, and UL33. X - Slime mold cyclic AMP receptor. X XThe structure of all these receptors is thought to be identical: they have Xseven hydrophobic regions, each of which most probably spans the membrane. XThe N-terminus is located on the extracellular side of the membrane, and is Xglycosylated, while the C-terminus is cytoplasmic and phosphorylated. Three Xextracellular loops alternate with three intracellular loops to link the Xseven transmembrane regions. The most conserved parts of all these proteins Xare the transmembrane regions and the first two cytoplasmic loops. A conserved Xacidic-Arg-aromatic triplet is present in the N-terminal extremity of the Xsecond cytoplasmic loop [15], it could be implicated in the interaction with G Xproteins. X XTo detect this widespread family of proteins we have developed a pattern that Xcontains the conserved triplet and that also spans the major part of the third Xtransmembrane helix. X X-Consensus pattern: [GSTALIVMC]-[GSTAPDE]-{EDPKRH}-x(2)-[LIVMNG]-x(2)- X [LIVMFT]-[GSTAN]-[LIVMFYWAS]-[DEN]-R-[FYWCH]-x(2)-[LIVM] X-Sequences known to belong to this class detected by the pattern: ALL, except X for slime mold cAMP receptor which does not seem to really belong to the R7G X family. X-Other sequence(s) detected in SWISS-PROT: Drosophila insulinase. X X-Expert(s) to contact by email: Chollet A. X chollet@clients.switch.ch X Attwood T.K. X bph6tka@biovax.leeds.ac.uk X X-Last update: December 1991 / Pattern and text revised. X X[ 1] Strosberg A.D. X Eur. J. Biochem. 196:1-10(1991). X[ 2] Kerlavage A.R. X Curr. Opin. Struct. Biol. 1:394-401(1991). X[ 3] Hartig P.R. X Trends Pharmacol. Sci. 10:64-69(1989). X[ 4] Libert F., Schiffmann S.N., Lefort A., Parmentier M., Gerard C., X Dumont J.E., Vanderhaeghen J.-J., Vassart G. X EMBO J. 10:1677-1682(1991). X[ 5] Friell T., Kobilka B.K., Lefkowitz R.J., Caron M.G. X Trends Neurosci. 11:321-324(1988). X[ 6] Gerard N.P., Gerard C. X Nature 349:614-617(1991). X[ 7] Stevens C.F. X Curr. Biol. 1:20-22(1991). X[ 8] Vane J. X Nature 348:673-673(1990). X[ 9] Salesse R., Remy J.J., Levin J.M., Jallal B., Garnier J. X Biochimie 73:109-120(1991). X[10] Gantz I., Schaffer M., Delvalle J., Logsdon C., Campbell V., Uhler M., X Yamada T. X Proc. Natl. Acad. Sci. U.S.A. 88:429-433(1991). X[11] Buck L., Axel R. X Cell 65:175-187(1991). X[12] Honda Z.-I., Nakamura M., Miki I., Minami M., Watanabe T., Seyama Y., X Okado H., Toh H., Ito K., Miyamoto T., Shimizu T. X Nature 349:342-346(1991). X[13] Hirata M., Hayashi Y., Ushikubi F., Yokota Y., Kageyama R., Nakanishi S., X Narumiya S. X Nature 349:617-620(1991). X[14] Applebury M.L., Hargrave P.A. X Vision Res. 26:1881-1895(1986). X[15] Attwood T.K., Eliopoulos E.E., Findlay J.B.C. X Gene 98:153-159(1991). X{END} X{PDOC00211} X{PS00238; OPSIN} X{BEGIN} X************************************************* X* Visual pigments (opsins) retinal binding site * X************************************************* X XVisual pigments [1,2] are the light-absorbing molecules that mediate vision. XThey consist of an apoprotein, opsin, covalently linked to the chromophore Xcis-retinal. Vision is effected trough the absorption of a photon by cis- Xretinal which is isomerized to trans-retinal. This isomerization leads to a Xchange of conformation of the protein. Opsins are integral membrane proteins Xwith seven transmembrane regions. The attachment site for retinal is a Xconserved lysine residue in the middle of the seventh transmembrane helix. X XIn vertebrates there are four different pigments. Cone cells, which function Xin bright light, are responsible for color vision and contain the three color Xpigments (red, blue and green). Rod cells, which mediate vision in dim light, Xcontain the fourth pigment, rhodopsin. The sequence of all three human cone Xcolor opsins is known, and rhodopsin has been sequenced in mammals as well as Xin various other species such as chicken, octopus, or lamprey [3]. X XIn Drosophila, the eye is composed of 800 facets or ommatidia. Each Xommatidium contains eight photoreceptor cells (R1-R8): the R1 to R6 cells are Xouter cells, while R7 and R8 are inner cells. Each of the three types of Xcells (R1-R6, R7 and R8) expresses a specific opsin. X XWe developed a pattern which includes the retinal binding lysine and which Xallows the specific detection of opsins. X X-Consensus pattern: K-x(5)-[DN]-P-x-[IV]-Y-x(6)-[FY] X [K is the retinal binding site] X-Sequences known to belong to this class detected by the pattern: ALL. X-Other sequence(s) detected in SWISS-PROT: NONE. X-Last update: December 1991 / Text revised. X X[ 1] Applebury M.L., Hargrave P.A. X Vision Res. 26:1881-1895(1986). X[ 2] Fryxell K.J., Meyerowitz E.M. X J. Mol. Evol. 33:367-378(1991). X[ 3] Hisatomi O., Iwasa T., Tokunaga F., Yasui A. X Biochem. Biophys. Res. Commun. 174:1125-1132(1991). X{END} END_OF_FILE if test 15369 -ne `wc -c <'ProSearch2.0/test.out'`; then echo shar: \"'ProSearch2.0/test.out'\" unpacked with wrong size! fi # end of 'ProSearch2.0/test.out' fi if test -f 'ProSearch2.0/test.pep' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'ProSearch2.0/test.pep'\" else echo shar: Extracting \"'ProSearch2.0/test.pep'\" \(375 characters\) sed "s/^X//" >'ProSearch2.0/test.pep' <<'END_OF_FILE' X> bov.ops 348 bases XMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIML XGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH XGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE XNHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNN XESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV XTRMVIIMVIAFLICWLPYAGVAFYIFTHQGFDFGPIFMTIPAFFAKTSAV XYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA END_OF_FILE if test 375 -ne `wc -c <'ProSearch2.0/test.pep'`; then echo shar: \"'ProSearch2.0/test.pep'\" unpacked with wrong size! fi # end of 'ProSearch2.0/test.pep' fi echo shar: End of shell archive. exit 0 -- Frank Kolakowski ======================================================================= O Email: lfk@eastman1.mit.edu or kolakowski@helix.mgh.harvard.edu O O US Mail: Lee F. Kolakowski Endocrine Unit O O Massachusetts General Hospital Wellman 5 O O Boston, MA 02114 Phone AT&T: 1-617-726-3966 O =======================================================================