From owner-srs@net.bio.net Mon Nov 06 22:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!sun4nl!sci.kun.nl!caos.kun.nl!schaft From: schaft@caos.kun.nl (Gijs Schaftenaar) Subject: srstk bug when using tk4.0 Message-ID: <1995Nov7.104258.21106@caos.kun.nl> Organization: CAOS/CAMM Date: Tue, 7 Nov 1995 10:42:58 GMT Lines: 47 SRSTK bug When using srstk with tk4.0 and higher, the following problem could occur: Selecting a query set from the query sets listbox where already one set was selected would result in two sets to be selected, where the rest of the program expects just one set to be selected. To correct this change in the file "srstk.tcl" at line 178: old: if {$oldTK} { set selcomm "select from" } else { set selcomm "selection set" } bind .query.qhist.fr.list \ "%W $selcomm \[%W nearest %y\] ;SelField .mbar.fields.menu \$Set Dbs(\[SelSet .query.qhist.fr.list\])" New: set bcomm \ {SelField .mbar.fields.menu $SetDbs([SelSet .query.qhist.fr.list])} if {$oldTK} { bind .query.qhist.fr.list \ "%W select from \[%W nearest %y\] ; $bcomm" } else { bind .query.qhist.fr.list \ "%W selection clear 0 end; %W selection set \[%W nearest %y\] ; $bcomm" } ================================================== Regards Gijs +----------------------------+-----------------------------------+ Gijs Schaftenaar, Drs. | CAOS/CAMM Center Email: schaft@caos.kun.nl | University of Nijmegen URL : http://www.caos.kun.nl/staff/schaft.html Tel. : +31 80 65 33 69 | Toernooiveld 1 Fax : +31 80 65 29 77 | 6525 ED Nijmegen, The Netherlands +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+ From owner-srs@net.bio.net Sat Nov 18 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: IMPORTANT: BIOSCI miniFAQ Date: 19 Nov 1995 02:00:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511191000.CAA28443@net.bio.net> NNTP-Posting-Host: net.bio.net This is a new "miniFAQ" designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the newsgroups from about 95% of the spams that are being sent to date. This means that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. 2) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-srs@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!in2.uu.net!caen!uwm.edu!lll-winken.llnl.gov!simtel!swidir.switch.ch!swsbe6.switch.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Copying SRS indexes between computers ? Date: 23 Nov 1995 11:01:37 GMT Organization: Belgian EMBnet Node Lines: 13 Message-ID: <491kah$2qe@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] We have two computers where SRS is running, a DEC OSF/1 and a slower DEC ULTRIX. With the increase of the databank sizes the DEC ULTRIX spends to much time making the indexes. Therefore I tried to ftp indexes from the OSF/1 machine to the ULTRIX machine. Now, SRS seems able to use the indexes to perform a search, but when srscheck is run, it does not see the indexes, and wants to reindex. A few questions for the SRS gurus : What criteria besides the date of creation of the index files does srscheck use to decide if an index must be remade ? Is an index made on one computer fully usable on another ? And if so, should the ftp be performed in ascii or binary mode ? Guy Bottu From owner-srs@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!usc!elroy.jpl.nasa.gov!lll-winken.llnl.gov!uwm.edu!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: Copying SRS indexes between computers ? Date: 23 Nov 1995 13:02:46 GMT Organization: Biology, Indiana University - Bloomington Lines: 24 Message-ID: <491rdm$e0u@usenet.ucs.indiana.edu> References: <491kah$2qe@rc1.vub.ac.be> NNTP-Posting-Host: sunflower.bio.indiana.edu There is/was a bug in SRS (version 4.02?) in Unix file date checking. On the version I work with, SRS was checking the file "ctime" or change time, not the file "mtime" modify time. I'm not sure if this is the problem you ran into, but I would guess so. I do copy SRS indices among unix (sun) computers and use them. My cure was, in file srs/src/tm.c, function TimeFileCreate change the returned time from "st_ctime" to "st_mtime" like this: fstat (fileNo, &buff); return buff.st_mtime; /* dgg, was ctime (status change time, bad) */ In article <491kah$2qe@rc1.vub.ac.be>, Guy Bottu wrote: >We have two computers where SRS is running, a DEC OSF/1 and a slower >DEC ULTRIX. With the increase of the databank sizes the DEC ULTRIX >spends to much time making the indexes. Therefore I tried to ftp >indexes from the OSF/1 machine to the ULTRIX machine. Now, SRS seems >able to use the indexes to perform a search, but when srscheck is run, >it does not see the indexes, and wants to reindex. ... -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: Retrieving features with SRS : the problem (part 2!) Date: 23 Nov 1995 15:29:00 GMT Organization: Belgian EMBnet Node Lines: 7 Message-ID: <4923vs$5vv@rc1.vub.ac.be> References: <45g92s$51v@rc1.vub.ac.be> <463e8b$5o1@hermod.uio.no> <1995Oct25.160829.24801@caos.kun.nl> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] thanks ! By the way, I see that Thure Etzold has already entered this bug fix in release 4.8 of his software distribution. and now the other bug which occurs when there are several features to be retrieved in the same sequence... Guy Bottu From owner-srs@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Norway.EU.net!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: Copying SRS indexes between computers ? Date: 23 Nov 1995 15:47:35 GMT Organization: The Sanger Centre Lines: 20 Message-ID: References: <491kah$2qe@rc1.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: gbottu@ben.vub.ac.be's message of 23 Nov 1995 11:01:37 GMT In article <491kah$2qe@rc1.vub.ac.be> gbottu@ben.vub.ac.be (Guy Bottu) writes: > A few questions for the SRS gurus : What criteria besides the date of > creation of the index files does srscheck use to decide if an index > must be remade ? Is an index made on one computer fully usable on another ? > And if so, should the ftp be performed in ascii or binary mode ? We use the same index files over NFS on Irix, OSF and Solaris (well, not sure whether anyone really uses them on Solaris, but certainly on the other two). No copying, no problems - but you do get trouble with the index dates if you tar/untar or copy the files. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Sat Nov 25 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!EU.net!Portugal.EU.net!news.rccn.net!scsing.switch.ch!swsbe6.switch.ch!news.vub.ac.be!ben!rherzog From: rherzog@ben.vub.ac.be (Robert Herzog) Newsgroups: bionet.software.srs Subject: Funny CDS from srs... Date: 25 Nov 1995 23:33:19 GMT Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 26 Message-ID: <49893v$hs9@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] Hello, I have been extracting several hundreds of CDS from various sequences lately, i and found a funny extraction from the MIDMM1 file (from Drosophila) : the second CDS srs extracts is as follows: MIDMM1 Length: 1536 Check: 5450 .. 1 @M@CGACAAT GATTATTTTC TACAAATCAT AAAGATATTG GAACTTTATA TTTTATTTTT 61 GGAGCTTGAG CTGGAATAGT TGGAACATCT TTAAGAATTT TAATTCGAGC TGAATTAGGA 121 CATCCTGGAG CATTAATTGG AGATGATCAA ATTTATAATG TAATTGTAAC TGCACATGCT 181 TTTATTATAA TTTTTTTTAT GGTTATACCT ATTATAATTG GTGGATTTGG AAATTGATTA two or three unusual bases at the start of this one...! This sequence is from a GCG file, out of which a lookup produces the proper data. I get the error with SRSWWW as well as with the vt100 version (rel 4.08). I tried this query out of another srswww server (Basel) and found the same error as from our's. What is wrong ? Robert Herzog From owner-srs@net.bio.net Sun Nov 26 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!usenet From: Robert Herzog Newsgroups: bionet.software.srs Subject: Re: Funny CDS from srs... More comments... Date: 27 Nov 1995 21:13:18 GMT Organization: Université libre de bruxelles Lines: 53 Message-ID: <49d9le$k9d@rc1.vub.ac.be> References: <49893v$hs9@rc1.vub.ac.be> NNTP-Posting-Host: isdn_pc2.ulb.ac.be. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) To: pmr@sanger.ac.uk There is something going wrong here: In the record from Genbank, the translation looks correct : a bona fide peptide of a few hundred amino acids long. But SRS seems to confuse the "W" and the "*", as each (or most, I did not check everything ;-) W appears like the translation of a stop codon. Here a copy from the SRS query at Darasbury (we do not keep a full Genbank under SRS at BEN today): LOCUS DROMTM1 5292 bp DNA INV 20-SEP-1995 DEFINITION Drosophila melanogaster mitochondrial cytochrome c oxidase subunits, ATPase6, 7 tRNAs (Trp, Cys, Tyr, Leu(UUR), Lys, Asp, Gly) genes, and unidentified reading frames A6l, 2 and 3. CDS_pept 1071. .2606 /note="NCBI gi: 903727" /codon_start=1 /transl_except=(pos:1071. .1073,aa:Met) /transl_table=5 /product="cytochrome c oxidase I" /translation="MRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGA LIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWL LPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAV NFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFF DPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAML AIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSP AILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFI HWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNI VSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPL LTN" CC translation with default table (experimental) >DROMTM1 MRQ*LFSTNH KDIGTLYFIF GA*AGIVGTS LRILIRAELG HPGALIGDDQ IYNVIVTAHA FIIIFFMVIP IIIGGFGN*L VPLILGAPDI AFPRINNIRF *LLPPALSLL LVSRIVENGA GTG*TVYPPL SAGIAHGGAS VDLAIFSLHL AGISSILGAV NFITTVINIR STGISLDRIP LFV*SVVITA LLLLLSLPVL AGAITILLTD RNLNTSFFDP AGGGDPILYQ HLF*FFGHPE VYILILPGFG IISHIIRQES GKKETFGSLG IIYAILAIGL LGFIV*AHHI FTVGIDVDTR AYFTSATIII AVPTGIKIFS *LATLHGTQL SYSPAIL*AL GFVFLFTVGG LTGVVLANSS VDIILHDTYY VVAHFHYVLS IGAVFAIIAG FIH*YPLFTG LTLNNK*LKS HFIIIFIGVN LTFFPQHFLG LAGIPRRYSD YPDAYTT*NI VSTIGSTISL LGILFFFFII *ESLVSQRQV IYPIQLNSSI E*YQNTPPAE HRYSELPLLT N From owner-srs@net.bio.net Sun Nov 26 22:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: Funny CDS from srs... Date: 27 Nov 1995 09:45:51 GMT Organization: The Sanger Centre Lines: 41 Message-ID: References: <49893v$hs9@rc1.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: rherzog@ben.vub.ac.be's message of 25 Nov 1995 23:33:19 GMT In article <49893v$hs9@rc1.vub.ac.be> rherzog@ben.vub.ac.be (Robert Herzog) writes: > I have been extracting several hundreds of CDS from various sequences lately, i > and found a funny extraction from the MIDMM1 file (from Drosophila) : > > the second CDS srs extracts is as follows: > > MIDMM1 Length: 1536 Check: 5450 .. > > 1 @M@CGACAAT GATTATTTTC TACAAATCAT AAAGATATTG GAACTTTATA TTTTATTTTT > 61 GGAGCTTGAG CTGGAATAGT TGGAACATCT TTAAGAATTT TAATTCGAGC TGAATTAGGA > 121 CATCCTGGAG CATTAATTGG AGATGATCAA ATTTATAATG TAATTGTAAC TGCACATGCT > 181 TTTATTATAA TTTTTTTTAT GGTTATACCT ATTATAATTG GTGGATTTGG AAATTGATTA > > two or three unusual bases at the start of this one...! Probably connected with trying to get a translation of it, bacause the feature table entry is: FT CDS 1071..2606 FT /note="NCBI gi: 903727" /codon_start=1 FT /transl_except=(pos:1071..1073,aa:Met) FT /transl_table=5 /product="cytochrome c oxidase I" Translation exception handling is in function SlbDoTranslExcept in seqlib.c, and puts "@X@" into the codon where "X" is the correct amino acid code. Of course, this should not happen for display of the sequence, only for translation. Seems to me that getz does not do translations anyway. certainly this code should be executed only if needed. I am not at all surprised LookUp is different - it seems to be a rather dated SRS version. I am still looking for signs of what GCG added (rather than the many things left out) in LookUp. -- ------------------------------------------------------------------------ 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 Nov 27 22:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: Funny CDS from srs... More comments... Date: 28 Nov 1995 09:53:38 GMT Organization: The Sanger Centre Lines: 54 Message-ID: References: <49893v$hs9@rc1.vub.ac.be> <49d9le$k9d@rc1.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Robert Herzog's message of 27 Nov 1995 21:13:18 GMT In article <49d9le$k9d@rc1.vub.ac.be> Robert Herzog writes: > There is something going wrong here: > In the record from Genbank, the translation looks correct : a bona fide > peptide of a few hundred amino acids long. But SRS seems to confuse the "W" > and the "*", as each (or most, I did not check everything ;-) W appears > like the translation of a stop codon. > > Here a copy from the SRS query at Darasbury (we do not keep a full Genbank > under SRS at BEN today): > > LOCUS DROMTM1 5292 bp DNA INV 20-SEP-1995 > DEFINITION Drosophila melanogaster mitochondrial cytochrome c oxidase > subunits, ATPase6, 7 tRNAs (Trp, Cys, Tyr, Leu(UUR), Lys, Asp, > Gly) > genes, and unidentified reading frames A6l, 2 and 3. > CDS_pept 1071. .2606 > /note="NCBI gi: 903727" > /codon_start=1 > /transl_except=(pos:1071. .1073,aa:Met) > /transl_table=5 > /product="cytochrome c oxidase I" That's because it's a mitochondrial sequence where one of the stop codons codes for Tryptophan instead. This is supposed to be what the "/transl_table=5" means, but I do not know of many programs that use it. It refers to NCBI translation table 5, which they also call "SGC4", so it appears in EGCG's EGenRunData directory as "trans4.txt". I suppose SRS could try to handle it - yet another of those dreadful feature table parsing problems where inconsistency in the feature table made it not worth designing software to cope with the many different possibilities. I seem to recall that /transl_table was going to be hidden somewhere (on the source key?) and not necessarily on every CDS (to reduce redundancy). There was even talk of leaving it out, and assuming all programs would be generating it from the taxonomy. The situation is still just as confused today. A quick check through the EMBL organelles file shows there is still no consistency in the annotation. I suggest, if you want to work with translated mitochondrial genes, that you should do the translations yourself to be sure you know what you are getting. -- ------------------------------------------------------------------------ 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 Tue Nov 28 22:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: embnet.general,bionet.software.srs Subject: Re: Swissprot? Date: 29 Nov 1995 13:31:46 GMT Organization: The Sanger Centre Lines: 20 Message-ID: References: <1995Nov28.171324.4496@comp.bioz.unibas.ch> <1995Nov29.112647.690@caos.kun.nl> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Jack Leunissen's message of Wed, 29 Nov 1995 11:26:47 GMT In article <1995Nov29.112647.690@caos.kun.nl> Jack Leunissen writes: >I know its not a big deal, and only matters for linking SRS, but I would have >appreciated that this had been announced somewhere; I might have adapted the >hyperlinks in SRS in time (hence the cross-post to bionet.software.gcg :-). Sorry, I don't see the connection between SRS hyperlinks and GCG. LookUp doesn't have HyperLinks. Just normal links, which should be through the accession number field and unaffected (though I avoid LookUp so I'm no expert). I *like* the new SWISS-PROT DR lines. About time - I have needed them for years, but better late than never. -- ------------------------------------------------------------------------ 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 Tue Nov 28 22:00:00 1995 Newsgroups: embnet.general,bionet.software.srs Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!sun4nl!sci.kun.nl!caos.kun.nl!root From: Jack Leunissen Subject: Re: Swissprot? Content-Type: text/plain; charset=us-ascii Message-ID: <1995Nov29.112647.690@caos.kun.nl> Sender: root@caos.kun.nl (System PRIVILEGED Account) Nntp-Posting-Host: cammsg1.caos.kun.nl Content-Transfer-Encoding: 7bit Organization: CAOS/CAMM Center References: <1995Nov28.171324.4496@comp.bioz.unibas.ch> Mime-Version: 1.0 Date: Wed, 29 Nov 1995 11:26:47 GMT X-Mailer: Mozilla 1.12 (X11; I; IRIX 5.3 IP19) X-Url: news://camms1.caos.kun.nl/1995Nov28.171324.4496@comp.bioz.unibas.ch Lines: 37 doelz@comp.bioz.unibas.ch (Reinhard Doelz) wrote: > >I am not aware that we (EMBnet) or other customers have been informed >on the status of the SWISSPROT database. All I have are files dated from >March 20, 1995 (8 months ago). I phoned EBI today and got the answer that >it should be known by now what reasons have caused to skip one release. >Even if this were true (one release overdue then by 1+ months), I would >prefer to get an official note from the EBI distribution channel what to >expect and how much the delay/volume discrepancy will be compared to >MIPS/PIR International. Ist there still a collaboration going on >amongst PIR and EMBL? How is the redundancy problem tackled there? Even then, I could live with that, as long I can *rely* on regular updates, with a *fixed* format. But what is happening to the cross-reference lines in SWISS-PROT? Looks like they (at least for EMBL) no longer give accession number AND ID-code, but accession number and the PID-number, as can be found in the CDS /note field. E.g. see the entry for CFTR_HUMAN in SWISSPROT: DR EMBL; M28668; HSCFTRM. and in SWISSNEW: DR EMBL; M28668; G180332; -. I know its not a big deal, and only matters for linking SRS, but I would have appreciated that this had been announced somewhere; I might have adapted the hyperlinks in SRS in time (hence the cross-post to bionet.software.gcg :-). Regards, Jack -- Jack A.M. Leunissen, PhD | CAOS/CAMM Center, Univ. of Nijmegen Email: jackl@caos.kun.nl | Toernooiveld Tel. : +31 24 365 22 48 | 6525 ED Nijmegen, The Netherlands Fax : +31 24 365 29 77 | URL=http://www.caos.kun.nl/ From owner-srs@net.bio.net Tue Nov 28 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!nntp.coast.net!oleane!jussieu.fr!univ-lille1.fr!u-strasbg.fr!pm7-0107-igbmc.u-strasbg.fr!plewniak From: Frederic PLEWNIAK Newsgroups: bionet.software.srs Subject: Re: Funny CDS from srs... Date: 28 Nov 1995 14:52:59 GMT Organization: IGBMC Lines: 28 Distribution: world Message-ID: <49f7ob$5dt@apopi.u-strasbg.fr> References: <49893v$hs9@rc1.vub.ac.be> NNTP-Posting-Host: pm7-0107-igbmc.u-strasbg.fr X-Newsreader: Nuntius Version 1.2 X-XXMessage-ID: X-XXDate: Tue, 28 Nov 1995 16:00:44 GMT In article <49d9le$k9d@rc1.vub.ac.be> Robert Herzog, rherzog@ulb.ac.be writes: > as each (or most, I did not check everything ;-) W appears > like the translation of a stop codon. > >Here a copy from the SRS query at Darasbury (we do not keep a full Genbank >under SRS at BEN today): > >LOCUS DROMTM1 5292 bp DNA INV 20-SEP-1995 >DEFINITION Drosophila melanogaster mitochondrial cytochrome c oxidase ^^^^^^^^^^^^^^^^^^^^^^ (...) > /transl_table=5 ^ >CC translation with default table (experimental) ^^^^^^^^^^^^ That's simply because SRS uses the standard translation table... which shouldn't be here since we've got here a mitochondrial non-standard code where TGA translates to W. Fred From owner-srs@net.bio.net Wed Nov 29 22:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!bioftp.unibas.ch!schmitz From: schmitz@comp.bioz.unibas.ch (Michael Schmitz) Subject: Gurus: SRS coredumps on embl_cc.ids Message-ID: <1995Nov30.123712.16552@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Date: Thu, 30 Nov 1995 12:37:12 GMT Lines: 28 Hi SRS Gurus, I encountered a strange problem when building index files for the current EMBL release: srsbuild coredumps when building the embl_cc.ids file. At the time of the coredump, the file has the following size: > 151484416 Nov 30 13:19 srs/index/embl_cc.ids whereas the second-largest file is only 53 Meg in size. The error message complains about insufficient memory; this may explain the size of the partial index file to some extent. Is this memory-hogging behaviour normal?? Or has something changed with the embl sdl file (I am using the 4.06 files from our 'production' server for a experimental installation on our linux box; the index generation is running on a Dec2000) Listening for hints ... Michael Schmitz BioComputing Basel -- /////////////////////////////////////////////////////////////// // M. Schmitz, Dipl. Phys. // schmitz@comp.bioz.unibas.ch // // BioComputing, Biozentrum // // // University of Basel // Fax +41 / 61 267 20 78 //