From owner-srs@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software,bionet.software.gcg,bionet.software.staden,bionet.software.srs Subject: Re: Software to extract annotation fields from EMBL/GenBank entries. Date: 03 Jun 1996 15:49:48 GMT Organization: The Sanger Centre Lines: 68 Message-ID: References: NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: b.robertson@ic.ac.uk's message of Mon, 03 Jun 1996 14:09:53 +0100 Xref: biosci bionet.software:15679 bionet.software.gcg:1826 bionet.software.staden:196 bionet.software.srs:260 In article b.robertson@ic.ac.uk (Brian Robertson) writes: > The amount of bacterial genome data available as sequenced cosmids of > 30-40 kb is increasing rapidly. Our problem is that we need to keep track > of newly discovered genes as they appear, so they can be incorporated into > our research program as appropriate. For this we need to create lists of > probable genes identified in the annotations for each cosmid. This can > then be circulated to laboratory workers. > > An example of this kind of annotation is shown below. We would like to > extract the "/note" field, which contains the probable function of the > gene, and create a list of these for each cosmid. >FT CDS_pept complement(3043..4155) >FT /note="MTCY190.03c, probable anthranilate >FT phosphoribosyltransferase, trpD, len: 370, similar to eg >FT SW:TRPD_LACCA P17170, (43.2% identity in 308 aa overlap), >FT initiation codon uncertain, gtg at 4086 favoured by >FT homology but this has no clear ribosome binding site" Clearly a job for SRS and ICARUS. Try the bionet.software.srs newsgroup (this message is crossposted there) ... But beware - these fields are often describing homologies rather than confirmed functional assignments (how firm the assignments are depends from project to project). Also, different projects will use different methods for formatting the initial annotation. There is as yet no consensus on how the data should be presented. Then again, you also need to keep up with changes to the entries in case the annotation includes a new homology, or the predicted gene changes (splice sites in eukaryotes, or the gtg alternative start codon in the example you used) >If a shell script is required, can anyone help with writing one? I'm >afraid it's beyond my capabilities..... Sadly, it's a little more complicated than that :-) What SRS can do is extract the features of interest for new/changed entries, for a given organism, since the last run. Something like: % getz "([emnew-org:Mycobacterium tuberculosis] & \ [emnew-dat#19960500:])" \ -f 'id acc dat def fts' >! mtcds.may96 ... which takes only a second or two to run. You can also do the same query through any of the SRSWWW servers (it will work on EMNEW or on GBNEW, updates for EMBL or GenBank). ICARUS in turn can be used to parse out the feature table fields of interest, assuming that all entries have some common format (in this case, all orf names start MTC but you could also look for "/gene=" to pick other entries). ICARUS is due sometime soon (in SRS 5). Meanwhile, other languages like Perl can do the job, although they are a little more complicated to write. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.tamu.edu!keck.tamu.edu!ajackson From: "Andrew J. Jackson" Newsgroups: bionet.software.srs Subject: Installing SRS v4.08 on SunOS Date: Tue, 4 Jun 1996 09:47:58 -0500 Organization: Texas A&M University, College Station, TX Lines: 77 Message-ID: NNTP-Posting-Host: keck.tamu.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I'm attempting to install SRS v4.08 on a SPARCstation 10 running SunOS4.1.3 and decided to use the gcc compiler. It does not finish the compiling process ("srsinstall all") because it complains about printf being undeclared. Here's the output: ----- Begin Included File ----- press RETURN to continue: ...updating file prep_srs enter the make command [make]: enter the cc command [cc]: gcc ...inserting commands "make" and "gcc" into srsmake for SunOS *** Welcome to SRS, version 4.08 *** *** make ODD-Compiler ..... make for SunOS with parameters: odd make: `/usr/software/srs4_08/bin/sunos/odd' is up to date. the end *** make objectbase (section) ..... ............ ............ ..................................... ..................................... ________________________________________________________________________________ made section files: "SRSSEC:srswin.sec" with 357 blocks "SRSSEC:srswin.ptr" with 80 blocks from input: "SRSSDL:srswin.sdl" defined 1197 objects of 27 different classes _______________________________________________________________________________ *** make index builder ..... make for SunOS with parameters: srsbuild make: `/usr/software/srs4_08/bin/sunos/srsbuild' is up to date. the end *** make index checker ..... make for SunOS with parameters: srscheck make: `/usr/software/srs4_08/bin/sunos/srscheck' is up to date. the end *** make header file: srsenv.h ..... *** make getz (retrieval program) ..... make for SunOS with parameters: getz gcc -Dsun -I/usr/software/srs4_08/bin/sunos -g -DSRSINCLUDE=\"srswin.h\" -c -o /usr/software/srs4_08/bin/sunos/getz.o getz.c getz.c: In function `main': getz.c:232: `printf' undeclared (first use this function) getz.c:232: (Each undeclared identifier is reported only once getz.c:232: for each function it appears in.) getz.c:236: `printf' used prior to declaration make: *** [/usr/software/srs4_08/bin/sunos/getz.o] Error 1 the end NEXT STEPS TO DO: ----------------- source etc/prep_srs srscheck srsupdate ----- End Included File ----- I've been looking at it too long and am at a point where I need another pair of eyes and brains to figure out the obvious. Thanks! -- Andrew J. Jackson W. M. Keck Center for Genome Informatics ajackson@keck.tamu.edu Texas A&M Univeristy Programmer/Analyst Institute of Biosciences & Technology Houston, TX From owner-srs@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!newsfeed.internetmci.com!news.wwa.com!news.ucdavis.edu!quad!knight From: knight@quad.cs.ucdavis.edu (James Knight) Newsgroups: bionet.software,bionet.software.gcg,bionet.software.staden,bionet.software.srs Subject: Re: Software to extract annotation fields from EMBL/GenBank entries. Followup-To: bionet.software,bionet.software.gcg,bionet.software.staden,bionet.software.srs Date: 6 Jun 1996 00:06:07 GMT Organization: University of California, Davis Lines: 138 Message-ID: <4p57df$35l@mark.ucdavis.edu> References: NNTP-Posting-Host: quad.cs.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:15715 bionet.software.gcg:1827 bionet.software.staden:197 bionet.software.srs:262 This type of problem is one of the reasons I wrote my SEQIO package. Below is a complete C program which will extract all of the /note fields from the CDS_pept features. The program takes a list of files and outputs the list of entries and the note fields as follows: For entry embl:MELLP late lactation protein precursor For entry embl:MEMRNAAL pot. alpha lactalbumin preprotein For entry embl:SC9920 YM9920.01c, unknown, partial, len: 956, CAI: 0.14; PS00061 Short-chain alcohol dehydrogenase family signature YM9920.02c, unknown, len: 61, CAI: 0.17, possible small spliced gene YM9920.03c, unknown, len: 55, CAI: 0.13, possible small spliced gene YM9920.04, unknown, len: 585, CAI: 0.18, putative glutamate decarboxylase gene It will also take care of splicing the lines together. It is, however, a little limited in that it can only handle EMBL format files, and it only looks for the /note field in each CDS_pept feature (these are fixed in the code). For someone with a little programming experience, it should be simple to modify the program to look for a different feature or a different sub-field of a feature. To compile the program, first extract the text from this message, then ftp my SEQIO package from the following site ftp://ftp.cs.ucdavis.edu/pub/strings/seqio.tar.gz unpack it, and compile the seqio.c and main program together using a C compiler. It should compile and run using any Unix or Windows NT/95 machine (in Windows, run the program from a DOS shell). (***Advertisement***) I wrote the SEQIO package for things just like this, where someone with a little programming experience needs to do something that no one has provided software for. The package simplifies all of the file and sequence I/O, so that the programmer can concentrate on the new piece of code. It's use does require C/C++ programming experience, but, as I hope you can see from the example below, not that much experience. (***End of Advert***) Jim #include #include #include #include #include "seqio.h" int main(int argc, char *argv[]) { int len, i, flag; char *entry, *s, *t, *s2, *t2, *feature, *note, *id; SEQFILE *sfp; for (i=1; i < argc; i++) { if ((sfp = seqfopen2(argv[i])) == NULL) continue; if (strcmp(seqfformat(sfp, 0), "EMBL") != 0) { fprintf(stderr, "%s: Not an EMBL file.\n", seqffilename(sfp, 0)); continue; } /* * Read the entries. */ while ((entry = seqfgetentry(sfp, &len, 0)) != NULL) { s = entry; flag = 0; while ((s = strstr(s, "\nFT CDS_pept")) != NULL) { /* * Found a CDS, so print the entry's id, if its the first CDS found. */ if (!flag) { if ((id = seqfmainid(sfp, 0)) != NULL || (id = seqfmainacc(sfp, 0))) printf("For entry %s\n", id); else printf("For an unknown entry\n"); flag = 1; } /* * Find the end of the feature lines for that CDS, and make * it NULL-terminated. */ feature = ++s; while (*s != '\n') s++; while (strncmp(s, "\nFT ", 6) == 0 && isspace(s[6])) { s++; while (*s != '\n') s++; } *s = '\0'; /* * Look for the /note field, then find the strings between * the quotes, squeezing out any line breaks. */ if ((t = strstr(feature, "/note=\"")) != NULL) { note = t2 = s2 = t + 7; while (s2 < s && *s2 != '"') { if (*s2 == '\n') { s2 += 6; /* Skip the "\nFT " and then the spaces */ while (*s2 != '\n' && isspace(*s2)) s2++; *t2++ = ' '; } else { if (t2 != s2) *t2 = *s2; t2++; s2++; } } *t2 = '\0'; printf(" %s\n", note); } *s = '\n'; } } seqfclose(sfp); } return 0; } From owner-srs@net.bio.net Tue Jun 18 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 19 Jun 1996 02:00:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199606190900.CAA05708@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-srs@net.bio.net Sun Jun 23 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!nntp.uio.no!news.cais.net!newsfeed.internetmci.com!in1.uu.net!news.puc.cl!macal20.facea.puc.cl!user From: mdin@puc.cl (test) Newsgroups: bionet.software.srs Subject: test Followup-To: bionet.software.srs Date: 24 Jun 1996 21:23:31 GMT Organization: nonr Lines: 1 Distribution: world Message-ID: NNTP-Posting-Host: macal20.facea.puc.cl Sorry, I can't get a better place at cyberspace to post that stuff From owner-srs@net.bio.net Mon Jun 24 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!enews.sgi.com!sgigate.sgi.com!nntp.coast.net!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: transfac accession query off by one Date: 25 Jun 1996 01:14:36 GMT Organization: Biology, Indiana University - Bloomington Lines: 9 Message-ID: <4qnehs$1nn@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu i tried installing transfac data into srs4 today, and found that accession number queries are off by one (query for R02509 returns R02508) and the acc num isn't listed in the report. this is using default transfac.sdl, and fiddling w/ that sdl didn't cure anything. same problems shows up at srs/ebi & srs/sanger. - don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Mon Jun 24 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: transfac accession query off by one Date: 25 Jun 1996 08:56:10 GMT Organization: The Sanger Centre Lines: 32 Message-ID: References: <4qnehs$1nn@usenet.ucs.indiana.edu> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: gilbertd@sunflower.bio.indiana.edu's message of 25 Jun 1996 01:14:36 GMT In article <4qnehs$1nn@usenet.ucs.indiana.edu> gilbertd@sunflower.bio.indiana.edu (Don Gilbert) writes: > i tried installing transfac data into srs4 today, and > found that accession number queries are off by one > (query for R02509 returns R02508) and the acc num isn't listed > in the report. this is using default transfac.sdl, and > fiddling w/ that sdl didn't cure anything. same problems > shows up at srs/ebi & srs/sanger. Oops. Thought I had caught those ones. Nope, I did it for RHDB and friends though. The problem seems to be databases like TFSITE (in this case) where the flat file has the accession number *before* the ID. This seems to mean that when the "AC RH02509" line is reached, the parser still thinks it is on the previous entry. The fix is probably to make the "AC" line the ID for the entry, and do something else with the ID line for now (I used "DF_NAM" for RHMAP). This makes the accession number show up as the entry name. Our transfac.sdl file has this change now, and seems to be OK on a quick test. No doubt fixed in SRS 5, but for now we have to work around as far as I can see. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambs, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Tue Jun 25 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!EU.net!news-res.gsl.net!news.gsl.net!nntp.coast.net!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!nntp Newsgroups: bionet.software.srs Subject: Lookup indices & native SRS Message-ID: <1996Jun26.121100.235@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 26 Jun 96 12:10:59 +0100 Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24 Lines: 16 Hello, I think this question has been addressed before but I couldn't find it anymore. So, is it possible to use the LookUp indices provided by GCG under SRS V4.08? If so, how? Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-srs@net.bio.net Wed Jun 26 23:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!news2.cais.net!news.cais.net!nntp.uio.no!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: This is the patch [Re: Lookup indices & native SRS] Message-ID: <1996Jun27.191533.2323@comp.bioz.unibas.ch> Organization: former EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <1996Jun26.121100.235@immunbio.mpg.de> Date: Thu, 27 Jun 1996 19:15:33 GMT Lines: 221 Michael Schmitz wrote: > > Christoph Gartmann (GARTMANN@IMMUNBIO.MPG.DE) wrote: > : Hello, > > : I think this question has been addressed before but I couldn't find it anymore. > : So, is it possible to use the LookUp indices provided by GCG under SRS V4.08? > : If so, how? > > As far as I remember, the problem discussed before was the opposite: using > existing SRS-build indices with Lookup. And that required changes to Lookup ... > > Michael Schmitz Hello, I don't remember the precise patch either, and as I moved to another site I had to do it again; admittedly I restrict this posting to UNIX by now. There are three problems with srs4_08 in GCG 8.1: 1) the GCG version is << 4.08 2) it can do only sequence libraries 3) building in GCG is not too trivial as it uses a complex makefile The strategy to make it work is as follows. I appreciate any feedback. Regards Reinhard 1) MAKE NORMAL NATIVE SRS ================================= Get srs4.08 and treat it as usual. Make sure that getz -libs gets you at least a single "sequence" type. % getz -libs Library Group Entries Index Date ------------------------------------------------------------------- SWISSPROT Sequence 52205 4/25/96 SWISSNEW Sequence 2819 4/25/96 PIR Sequence 82066 4/25/96 NRL3D Sequence 6063 4/26/96 ... 2) MAKE A NEW DIRECTORY AND GET THE GCG STUFF WORKING ============================================================= Make a new directory, move there, invoke GCG and GCGSUPPORT, and get gensource:lookup.c as usual: % fetch gensource:lookup.c Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. lookup.c Next, get the makefiles (fetch make*) and change the "name" c example in makefile.mm to "lookup". Make the makefile. The next is a crude hack and the GCG folks might correct me but this worked in my hands. Next, printenv the variable for the executable % printenv SRSEXE Edit the makefile and add the variable you got there (e.g. /sw/srs4_08/bin/irix) and add this to the 'include' section _before_ the other includes (this is extremely important as you will use GCVG's include otherwise). In my system this might look like CFLAGS = -Dirix -Dunix -D__LONGLONG -ansiposix -cckr -common $(DEBUGFLAGS) -I/sw/srs4_08/bin/irix -I$(IDIR) Do the same with the link library statement and add the need to add libsrs.a from your native SRS installation. CEXLIBS = -L/sw/srs4_08/bin/irix/ -lsrs -L$(LDIR) -lgenshare -l$(CURSES) -lm -lmalloc (remember that this must look different on your system as you will have the srs installation in a different path! Also, do not allow any space between -I and -L and the leading slash of the filename). Try it - don't get frustrated as it won't work but you should get something like % make lookup cc -Dirix -Dunix -D__LONGLONG -ansiposix -cckr -common -DNDEBUG -I/sw/srs4_08/bin/irix/ -I/bio1/gcg/gcg81/gcgsource/include -c lookup.c cc -DNDEBUG lookup.o /bio1/gcg/gcg81/gcgbin/oblib/libapp.a -L/sw/srs4_08/bin/irix/ -lsrs -L/bio1/gcg/gcg81/gcgbin/oblib -lgenshare -lcurses -lm -lmalloc -o lookup ld: Unresolved: MsgGetFnct *** Error code 1 3. MODIFY LOOKUP TO RUN ONLY SEQUENCE LIBRARIES =================================================== There are only three locations which you need to change. % diff lookup.c.patch lookup.c.orig 568a571 > if (!strcmp(g->com, "Sequence")) { 582c585 < --- > } 1702a1706,1712 > > static int (*PrintMessage)(MSGo *) = NULL; /* pointer to print function */ > > INT4 (*MsgGetFnct (void))() > { > return PrintMessage; > } The first is that in line 568 there is a loop which embraces all libraries. That's not what we need, as we got the group in the previous line the statement for(lcontext = 0; l = LibNextLib(g, &lcontext); needs only be executed if g->com is "sequence": 571 for(lcontext = 0; l = LibNextLib(g, &lcontext); ) { (gdb) p g $3 = (struct SRSoGROUP_ *) 0x10266404 (gdb) p *g $4 = {key = 0x1028033c "S", com = 0x10280330 "Sequence", short_nm = 0x10280340 "SQ", cmnt = 0x10280344 "Search sequence libraries", help = 0x10280360 "srs_me query lib", single_f = 0 '\000', library = {0x10264228, 0x102642c4, 0x102645d0, 0x10264360, 0x102643fc, 0x10264498, 0x10264708, 0x10265c5c, 0x10265cf8, 0x0 }, libraryN = 9, df_t = {0x102784ac, 0x10278484, 0x102784d4, 0x10278524, 0x1027854c, 0x10278574, 0x1027859c, 0x102785c4, 0x102785ec, 0x1027868c, 0x10278664, 0x10278614, 0x1027863c, 0x102784fc, 0x102786dc, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0}, upd_f = 0 '\000'} All what we do, therefore, is add the line if (!strcmp(g->com, "Sequence")) { before this line (after the line stating SLBo *l;) and end this condition just before the end of the main loop (stating } /* end loop */) with a single }. This passage should now look like for(count = 0, gcontext = 0; g = LibNextLibGroup(&gcontext);) { int lcontext; SLBo *l; if (!strcmp(g->com, "Sequence")) { for(lcontext = 0; l = LibNextLib(g, &lcontext); ) { [... some lines deleted deleted for clarity ...] if(!access(buf, R_OK)) activeLib[count++] = l; } } } /* end loop */ If you want to be really perfect and have more than 24 sequence libraries :-) you need to add a counter that tells the LibNextLib to stop after 23 readings but you'll miss all beyond this point. 4. ADD THE MISSING FUNCTION =============================== Last, we need to add the function MsgGetFnct and define PrintMessage as this got dropped at least in my 4.08 SRS native version. Append the lines static int (*PrintMessage)(MSGo *) = NULL; /* pointer to print function */ INT4 (*MsgGetFnct (void))() { return PrintMessage; } to lookup.c, exit the editor, and recompile with "make lookup". Try it out: % ./lookup LookUp identifies sequences by name, accession number, author, organism, keyword, title, reference, feature, definition, length, or date. The output is a list of sequences. The LookUp program is experimental in this release--please look carefully at your results. LOOKUP in what sequence libraries: a) swissprot b) swissnew ... m) All libraries n) quit Please choose one or more (* m *): 5. RETURN THE BINARY TO THE USUAL PLACE ============================================ Last, you need to copy the binary to the usual place % mv $GCGUTILDIR/lookup $GCGUTILDIR/lookup.orig % cp lookup $GCGUTILDIR/lookup and rescue the source code. DISCLAIMER ========== No warranty for this patch. This is an inofficial fix and neither myself nor GCG or my employer are responsible for this posting or any consequence arising thereof. [PS: Please don't use this message to reply:to as I don't read my mailbox at this address frequently. I've posted from my new address once earlier and you can get the mail address from there if you need] -- Reinhard Doelz, Basel, Switzerland From owner-srs@net.bio.net Wed Jun 26 23:00:00 1996 Path: biosci!rutgers!sgigate.sgi.com!swrinde!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!zrz.TU-Berlin.DE!cs.tu-berlin.de!uni-erlangen.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!nntp Newsgroups: bionet.software.srs Subject: Re: Lookup indices & native SRS Message-ID: <1996Jun27.174142.237@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 27 Jun 96 17:41:42 +0100 References: <1996Jun26.121100.235@immunbio.mpg.de> Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24 In-Reply-To: pmr@sanger.ac.uk's message of 27 Jun 1996 09:11:34 GMT Lines: 35 In pmr@sanger.ac.uk writes: > In article <1996Jun26.121100.235@immunbio.mpg.de> GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) writes: > > >I think this question has been addressed before but I couldn't find > >it anymore. > > > >So, is it possible to use the LookUp indices provided by GCG under > >SRS V4.08? > > Yes, but I don't think you would want to. > > GCG's indices have no links to databases like PROSITE (actually, they > don't even index prosite). Ok, so the next question is: as SRS creates separate indices for all the fields in a database (e.g. EMBL_AUT, EMBL_FTS,...), is it possible to use these and create links via native SRS? > A more reasonable question is "can I use my normal SRS 4.08 indices > with GCG?" to which the answer is "yes, but GCG doesn't make it easy." At the moment I don't provide LOOKUP to the users. I simply thought I could save time creating indices. Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-srs@net.bio.net Wed Jun 26 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!nowhere.uucp!schmitz Newsgroups: bionet.software.srs Subject: Re: Lookup indices & native SRS Message-ID: <1996Jun27.112837.46665@yogi.urz.unibas.ch> From: schmitz@comp.bioz.unibas.ch (Michael Schmitz) Date: 27 Jun 96 11:28:37 MET Reply-To: schmitz@bioa.embnet.unibas.ch References: <1996Jun26.121100.235@immunbio.mpg.de> Distribution: world Organization: Biocomputing, Biozentrum Basel Nntp-Posting-Host: biopcl.embnet.unibas.ch X-Newsreader: TIN [version 1.2 PL2] Lines: 11 Christoph Gartmann (GARTMANN@IMMUNBIO.MPG.DE) wrote: : Hello, : I think this question has been addressed before but I couldn't find it anymore. : So, is it possible to use the LookUp indices provided by GCG under SRS V4.08? : If so, how? As far as I remember, the problem discussed before was the opposite: using existing SRS-build indices with Lookup. And that required changes to Lookup ... Michael Schmitz From owner-srs@net.bio.net Wed Jun 26 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!nntp.coast.net!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: Lookup indices & native SRS Date: 27 Jun 1996 09:11:34 GMT Organization: The Sanger Centre Lines: 40 Distribution: world Message-ID: References: <1996Jun26.121100.235@immunbio.mpg.de> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: GARTMANN@IMMUNBIO.MPG.DE's message of 26 Jun 96 12:10:59 +0100 In article <1996Jun26.121100.235@immunbio.mpg.de> GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) writes: >I think this question has been addressed before but I couldn't find >it anymore. > >So, is it possible to use the LookUp indices provided by GCG under >SRS V4.08? Yes, but I don't think you would want to. GCG's indices have no links to databases like PROSITE (actually, they don't even index prosite). A more reasonable question is "can I use my normal SRS 4.08 indices with GCG?" to which the answer is "yes, but GCG doesn't make it easy." There are two fixes. One posted here some time ago by Reinhard Doelz, and another which I have hacked together here but not used much (I tell users to use getz instead of "LookUp" as GCG's LookUp makes no use of most of SRS anyway. The basic problem is that with all the usual SRS indices, GCG's menu blows up - also, GCG assumes that all SRS indexed databases are sequence ones. So, basically you have to tell LookUp to only use the sequence databases and ignore the rest. Oh yes, you also have to watch out for all those duplicated commands that GCG didn't rename: srsbuild, srscheck, odd I suggest keeping users away from LookUp, otherwise when SRS 5 and GCG 9 come along you could have an interesting time fixing it all over again. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambs, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England