From owner-srs@net.bio.net Fri Dec 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Funny CDS from srs... More comments... Date: Tue, 28 Nov 1995 17:14:01 +0100 Organization: EMBL Lines: 19 Distribution: world Message-ID: <30BB3549.77DA@EMBL-Heidelberg.DE> References: <49893v$hs9@rc1.vub.ac.be> <49d9le$k9d@rc1.vub.ac.be> NNTP-Posting-Host: pc-argos4.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b2 (Windows; I; 32bit) To: Peter Rice Peter Rice wrote: > > 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. whenever SRSWWW finds a CDS feature it replaces it by "CDS_pept" - the translate function uses currently only one translation table ...better translations can be found in TREMBL where the organism line is parsed and the appropriate table selected. we will fix this in srs5 where parsing is much easier regards thure From owner-srs@net.bio.net Fri Dec 01 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Gurus: SRS coredumps on embl_cc.ids Date: Thu, 30 Nov 1995 21:26:24 +0100 Organization: EMBL Lines: 29 Distribution: world Message-ID: <30BE1370.D3C@EMBL-Heidelberg.DE> References: <1995Nov30.123712.16552@comp.bioz.unibas.ch> NNTP-Posting-Host: pc-argos4.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b2 (Windows; I; 32bit) To: Michael Schmitz Michael Schmitz wrote: > 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. the indexing has not changed a bit since 4.01. The "cc" index is indeed by far the largest index of EMBL - one way to solve the problem would be to simply disable the indexing of the comment field. Another solution could be to improve the parser. One last suggestion: have you used unlimit before indexing? could be that the memory usage is simply limited. regards thure From owner-srs@net.bio.net Fri Dec 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Copying SRS indexes between computers ? Date: 24 Nov 1995 15:14:58 GMT Organization: EMBL Lines: 25 Distribution: world Message-ID: <494nhi$kcc@lion.embl-heidelberg.de> References: <491kah$2qe@rc1.vub.ac.be> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V2.0 alpha) X-URL: news:491kah$2qe@rc1.vub.ac.be When you copy or move files to another location the modification changes which makes srscheck believe that there is a new version of the databank. there is a special flag "-t" for srsbuild: srsbuild -t databankName sets the internal date of the indices to the current time so - if this happened after a 'move' - srscheck thinks the indices are current. unfortunately this does not affect the link indices ...but this don't yet have the indexing time internally - so it is safe to do touch *databankName*.lnk regards thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Sun Dec 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!EU.net!Norway.EU.net!nntp.uio.no!rodrigol From: rodrigol@biomaster.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: swissprot 32 Date: 4 Dec 1995 20:22:26 GMT Organization: University of Oslo, Norway Lines: 41 Message-ID: <49vla2$c3m@ratatosk.uio.no> NNTP-Posting-Host: biomaster.uio.no X-Newsreader: TIN [version 1.2 PL2] Hi! ( Warning: This message is intended to the SRS system administrator ) ( Disclaimer: All_disclaimers_applicable_and_possible) Some of you may have noticed that there are a few changes to Swissprot DR lines and that the link to medline are not working correctly. The change to the DR line has the effect of NOT getting me from my swissprot entry to the corresponding embl one since the link reads (looks after!) and embl-id and not an accession number. The fix to this is: file: hyperlink.sdl #linkcall /id=%FETCH_EMBL ! /call="%s" /call="%s" Also in hyperlink.sdl the Medline references can be fixed by: #hyperlink /field=@SWISSPROT_RX_FIELD ! /parse=swissprot_medline /parser=@INSERTLINK_PARSER /parse=lit_ref /parser=@INSERTLINK_PARSER Have a look at: http://bioslave.uio.no:8001/srs/srsc?-odd+hyperlink for further details. -- *************************************************************************** * RODRIGO LOPEZ SERRANO rodrigo.lopez@biotek.uio.no * * Norwegian EMBnet node Tel:xx-47-22958756 Fax:xx-47-22694130 * * http://www.no.embnet.org/ * *************************************************************************** From owner-srs@net.bio.net Mon Dec 04 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!Norway.EU.net!nntp.uio.no!rodrigol From: rodrigol@biomaster.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: tclcurses (FEATURE extraction problem) Date: 5 Dec 1995 08:23:09 GMT Organization: University of Oslo, Norway Lines: 20 Message-ID: <4a0vhd$h7m@ratatosk.uio.no> NNTP-Posting-Host: biomaster.uio.no X-Newsreader: TIN [version 1.2 PL2] Hi! Has anyone seen this and is there perhaps a fix for it? o Start the tclcurses interface. o Make a sequence query against swissprot o Chooce to search for features and type 'c2 & domain' (You should get 600 entries w/sw32) o List the entries o Show the first entry and you will see it twice, once for each C2 domain. This entry cannot be used unless one edits the output file to separate them. When you have 600 to go....:-( This is quite likely a bug. Could Gijs or someone from the CAOS/CAMM team have a look at this one? R:) From owner-srs@net.bio.net Tue Dec 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!nott!uottawa!mgcheo.med.uottawa.ca!sbaird From: sbaird@mgcheo.med.uottawa.ca (Stephen Baird) Newsgroups: bionet.software.srs Subject: srs4.08 install/objectbase problems Date: 6 Dec 1995 18:34:26 GMT Organization: University d'/of Ottawa Lines: 31 Message-ID: <4a4nni$29f8@mercury.cc.uottawa.ca> NNTP-Posting-Host: mgcheo.med.uottawa.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.1 PL8] Dear SRSers, I have SRS ver 4.08 and while doing the "srsinstall all" there seems to be a lot of problems with the paring elements in genbank.sdl and in the objectbase section I get ........e__symnotknown, symbol is not defined Line nr. 149 in file /seq/srs/srs4_08/odd/genbank.sdl symbol: @EM_SFT_FSTKEY e__bnfbuildfail, could not process Backus-Naur expressions before Line nr. 149 etc, etc. I can not see that I altered anything that would do this. Is this a 4.08 bug or have I done something wrong? Could it be because I am not including EMBL in the databases? Thanks, |--------------------------------------------------------------------| | Stephen Baird sbaird@mgcheo.med.uottawa.ca | | Molecular Genetics tel: 613-738-3925 | | Children's Hospital of Eastern Ontario fax: 613-738-4833 | | 401 Smyth Rd. | | Ottawa, Ontario | | Canada | | K1H 8L1 | |--------------------------------------------------------------------| From owner-srs@net.bio.net Sun Dec 10 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!nntp.coast.net!torn!news.unb.ca!nbt.nbnet.nb.ca!news From: "geneviève perron" Newsgroups: bionet.software.srs Subject: (no subject) Date: 11 Dec 1995 14:19:16 GMT Organization: NB*Net Lines: 4 Message-ID: <4ahel4$hn4@darwin.nbnet.nb.ca> NNTP-Posting-Host: 142.139.189.158 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) I would like to have any kind of information about software. Thank you Geneviève Perron From owner-srs@net.bio.net Mon Dec 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!natinst.com!news-relay.us.dell.com!swrinde!newsfeed.internetmci.com!chi-news.cic.net!nntp.coast.net!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: Re: tclcurses (FEATURE extraction problem) Date: 12 Dec 1995 09:32:05 GMT Organization: Belgian EMBnet Node Lines: 13 Message-ID: <4aji6l$hkn@rc1.vub.ac.be> References: <4a0vhd$h7m@ratatosk.uio.no> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] I had already noted a long time ago that srscurses and srstk fail to put the features in separate files when there are several features to be extracted from the same entry. Other problem is that srscurses and srstk create List Files with the SRS database names instead of the logical names defined in the odd files, so that they are unusable with GCG (fortunately we have lookup now). Also, srscurses cannot handle numeric fields. I am afraid that fixing this involves more than changing a few lines of code and that our collegues from CAOS/CAM have for the moment nobody to work full-time on it... Guy Bottu From owner-srs@net.bio.net Sun Dec 17 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!Germany.EU.net!news.dfn.de!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!uni-erlangen.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software.srs Subject: SRS V4.08 & VMS & EMBL Rel. 44 Message-ID: <1995Dec18.161326.208@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 18 Dec 95 16:13:25 +0100 Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24Lines: 26 Lines: 26 Hello, finally I decided to move from SRS V3.1 to V4.08 (under VMS) with EMBL Rel. 44. And now I cannot get SRSBUILD to create the indices for EMBL. After having processed around 190,000 entries the machine goes into an endless paging loop :-( The account under which SRSBUILD was run has all privileges, its paging file quota is set to the theoretical maximum as well as the system wide parameter. Only the page file itself is smaller and gets filled up completey (50 MB). With SRS V3.1 this was no problem. Thus, is there anybody who can provide me with some information on correct paramter settings? Do I have to change something in EMBL.SDL? Or can I ftp the index files for EMBL Rel. 44 in GCG format from some site? Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | 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 Mon Dec 18 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI miniFAQ, ver. 14-DEC-95 Date: 19 Dec 1995 02:00:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <199512191000.CAA03899@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-DEC-95) This BIOSCI "miniFAQ" is 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) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index in addition to the master index for the entire set. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all 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 USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, 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 on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface 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. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) 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. 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 Dec 20 22:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!EU.net!sun4nl!sci.kun.nl!caos.kun.nl!schaft From: schaft@caos.kun.nl (Gijs Schaftenaar) Subject: Re: tclcurses (FEATURE extraction problem) Message-ID: <1995Dec21.113534.14182@caos.kun.nl> Organization: CAOS/CAMM References: <4a0vhd$h7m@ratatosk.uio.no> <4aji6l$hkn@rc1.vub.ac.be> Date: Thu, 21 Dec 1995 11:35:34 GMT Lines: 39 gbottu@ben.vub.ac.be (Guy Bottu) writes: >I had already noted a long time ago that srscurses and srstk fail to >put the features in separate files when there are several features >to be extracted from the same entry. Other problem is that srscurses and >srstk create List Files with the SRS database names instead of the >logical names defined in the odd files, so that they are unusable >with GCG (fortunately we have lookup now). Also, srscurses cannot >handle numeric fields. >I am afraid that fixing this involves more than changing a few lines >of code and that our collegues from CAOS/CAM have for the moment >nobody to work full-time on it... > Guy Bottu I had already replied a long time ago to Guy that this is 'getz' behaviour and not 'srscurs' behaviour. (several features/database names) So if you want to complain about that, dont complain to me but to Thure. Putting in the numeric fields would be a lot of work. Thure and I agreed that major updates to the software would take new funding. So until that time you'd better use lookup. (PS: That is CAOS/CAMM) 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 Wed Dec 20 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!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: Re: tclcurses (FEATURE extraction problem) Date: 21 Dec 1995 15:31:53 GMT Organization: Belgian EMBnet Node Lines: 21 Message-ID: <4bbul9$ftd@rc1.vub.ac.be> References: <4a0vhd$h7m@ratatosk.uio.no> <4aji6l$hkn@rc1.vub.ac.be> <1995Dec21.113534.14182@caos.kun.nl> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] > I had already replied a long time ago to Guy that this is 'getz' behaviour > and not 'srscurs' behaviour. (several features/database names) > So if you want to complain about that, dont complain to me but to Thure. Indeed, I guess that if Thure added to the program getz a parameter -subn, like there is one in wgetz, it would be easy to adapt srscur and srstk. Meanwhile, the only (and awful) way to retrieve features in one move is to use the "naked" getz with commands of the type : getz -fosn -pos '[EMBL-ORG:LEGIONELLA PNEUMOPHILA] > [EMBL-FTS:CDS]' > Lpneu.list @Lpneu.list can be given as input to some GCG programs. Note that lookup (at least the present version under ULTRIX or OSF/1) gives a segmentation fault when you try to retrieve fragments.o On the other hand, that srscurs and srstk fail to use the GCG names of the databanks is not due to getz ! Guy Bottu From owner-srs@net.bio.net Wed Dec 27 22:00:00 1995 Path: biosci!agate!ihnp4.ucsd.edu!library.ucla.edu!newsfeed.internetmci.com!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!jussieu.fr!pasteur.fr!infobiogen.fr!news From: Jean-Marc Plaza Newsgroups: bionet.software.srs,bionet.molbio.embldatabank Subject: (no subject) Date: 28 Dec 1995 11:40:46 GMT Organization: INFOBIOGEN Lines: 106 Message-ID: <4btvnu$9qk@lovelace.infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4d) X-URL: news:bionet.software.srs Xref: biosci bionet.software.srs:205 bionet.molbio.embldatabank:582 Hi, there are several problems with EMBL 45 when you run trembl (Thure Etzold) on it. First, in CDS complement , trembl does a core dump when it finds : "complememt(>" instead of "complememt(" Secondly, The codon start for HSACTSG7 is /codon_start=2129 in EMBL 45 instead of 1, 2 or 3. And trembl does not like it -core dump. :-) In Genbank the codon start is /codon_start=1 for HUMACTSG7 and the translated sequence is different. Any idea to fix that ? Thanks Jean-Marc EMBL 45 ID HSACTSG7 standard; DNA; PRI; 466 BP. DE Human enteric smooth muscle gamma-actin gene, exon 9 and 3' flank. FT CDS_pept join(D00649:2129..2254,D00649:3135..3263,D00650:653..763, FT D00650:1033..1117,D00651:66..227,D00652:55..246,D00653:357 FT ..538,89..232) FT /note="gamma-actin precursor" FT /codon_start=2129 FT /db_xref="PID:e34116" FT /translation="PEWPQTASPWIRVVPWGIRRLLRFASMEYTKGKLPIFLAGNGMPVFT GEEADLFDDSVRVNYFNWYINEVLKAVKEDL= VDVRSYIVRSLIDGYEGPLGFSQRFGLYFT HVNFNDSSRPRTPRKSAYLFTSIIEKNGFSAKKVKRNPLPVRADFTSRARVTDSLPSEVFT PSK= AKISVEKFSKQPRFERDLFYDGRFRDDFLWGVSSSPYQIEGGWNADGKGPSIWDNFFT THTPGNGVKDNATGDVACDSYHQLDADLNILRTLKVKSYRFSISWSRIFPTGRNS= TINKFT QGVDYYNRLIDSLVDNNIFPMVTLFHWDLPQALQDIGGWENPSLIELFDSYADYCFKTFFT GDRVKFWMTFNEPWCHVVLGYSSGIFP= PSVQEPGWLPYKVSHIVIKAHARVYHTYDEKYFT RSEQKGVISLSLNTHWAEPKDPGLQRDVEAADRMLQFTMGWFAHPIFKNGDYPDVMKWTFT = VGNRSELQHLASSRLPTFTEEEKNYVRGTADVFCHNTYTSVFVQHSTPRLNPPSYDDDMFT ELKLIEMNSSTGVMHQDVPWGTRRLLNWIKEEYGNIPIYITENGQGLENPT= LDDTERIFFT YHKTYINEALKAYKLDGVDLRGYSAWTLMDDFEWLLGYTMRFGLYYVDFNHVSRPRTARFT ASARYYPDLIANNGMPLAREDEF= LYGEFPKGFIWSAASASYQVEGAWRADGKGLSIWDTFT FSHTPLRIGNDDNGDVACDSYHKIAEDVVALQNLGVSHYRFSIAWSRILPDGTTKFINEFT = AGLSYYVRFIDALLAAGITPQVTIYHWDLPQALQDVGGWENETIVQRFKEYADVLFQRLFT GDRVKFWITLNEPFVIAAQGYGTGVSAPGISFRPGTAPYIAGHNLIK= AHAEAWHLYNDVFT YRARQGGTISITISSDWGEPRDPTNREHVEAARSYVQFMGGWFAHPIFKNGDYPEVMKTFT RIRDRSLGAGLNKSRLPEF= TESEKSRIKGTFDFFGFNHNTTVLAYNLDYPAAFSSFDADFT RGVASIADSSWPVSGSFWLKVTPFGFRRILNWLKEEYNNPPIYVTENGVSRRGEPELNDFT = TDRIYYLRSYINEALKAVHDKVDLRGYTVWSIMDNFEWATGFAERFGVHFVNRSDPSLPFT RIPRASAKFYATIVRCNGFPDPAQGPHPCLQQPEDAAPTASPV= QSEVPFLGLMLGIAEAFT QTALYVLFALLLLGACSLAFLTYNTGRRSKQGNAQPSQHQLSPISSF"

ERROR:

syntax error, at "129 /db_xref="PID:e34116" /translation="PEWPQTASPWIRVVPWGIRRLLRFASMEYTKGKLPIFLAGNGM GENBANK 92 LOCUS HUMACTSG7 466 bp DNA PRI 23-JAN-1992 DEFINITION Human enteric smooth muscle gamma-actin gene, exon 9 and 3' flank. ACCESSION D00654 NID g219424 KEYWORDS actin; gamma-actin. SEGMENT 7 of 7 SOURCE Human peripheral blood genomic DNA, clone HACTSG-112. ORGANISM Homo sapiens Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Mammalia; Theria; Eutheria; Primates; Haplorhini; Catarrhini; Hominidae. REFERENCE 1 (bases 89 to 309) AUTHORS Miwa,T. and Kamada,S. TITLE The nucleotide sequence of a human smooth muscle (enteric type) gamma-actin cDNA JOURNAL Nucleic Acids Res. 18, 4263-4263 (1990) MEDLINE 90332437 REFERENCE 2 (bases 1 to 466) AUTHORS Miwa,T., Manabe,Y., Kurokawa,K., Kamada,S., Kanda,N., Bruns,G., Ueyama,H. and Kakunaga,T. TITLE Structure, chromosome location, and expression of the human smooth muscle (enteric type) gamma-actin gene: evolution of six human actin genes JOURNAL Mol. Cell. Biol. 11, 3296-3306 (1991) MEDLINE 91246198 COMMENT These data kindly submitted in computer readable form by: Takeshi Miwa Department of Oncogene Research Research Institute for Microbial Diseases Osaka University 3-1 Yamadaoka Suita Osaka 565 Japan Phone: 06-875-2470 Fax: 06-875-1292. NCBI gi: 219424 FEATURES Location/Qualifiers 1..466 /organism="Homo sapiens" CDS_pept join(D00649:2129..2254,D00649:3135..3263,D00650:653..763, D00650:1033..1117,D00651:66..227,D00652:55..246, D00653:357..538,89..232) /note="gamma-actin precursor; NCBI gi: 219426" /codon_start=1 /db_xref="PID:g219426" /translation="MCEEETTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGV MVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEH PTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGV THNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLC YVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIH ETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPP ERKYSVWIGGSILASLSTFQQMWISKPEYDEAGPSIVHRKCF" --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Wed Dec 27 22:00:00 1995 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.reston.ans.net!nntp.coast.net!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!jussieu.fr!pasteur.fr!infobiogen.fr!news From: Jean-Marc Plaza Newsgroups: bionet.molbio.embldatabank,bionet.software.srs Subject: trembl and EMBL 45 Date: 28 Dec 1995 11:43:50 GMT Organization: INFOBIOGEN Lines: 123 Message-ID: <4btvtm$9qk@lovelace.infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4d) X-URL: news:bionet.molbio.embldatabank?ALL Xref: biosci bionet.molbio.embldatabank:583 bionet.software.srs:206 Sorry, I forgot the subjecty so I post it again: Hi, there are several problems with EMBL 45 when you run trembl (Thure Etzold) on it. First, in CDS complement , trembl does a core dump when it finds : "complememt(>" instead of "complememt(" Secondly, The codon start for HSACTSG7 is /codon_start!29 in EMBL 45 instead of 1, 2 or 3. And trembl does not like it -core dump. :-) In Genbank the codon start is /codon_start=1 for HUMACTSG7 and the translated sequence is different. Any idea to fix that ? Thanks Jean-Marc EMBL 45 ID HSACTSG7 standard; DNA; PRI; 466 BP. DE Human enteric smooth muscle gamma-actin gene, exon 9 and 3' flank. FT CDS_pept join(D00649:2129..2254,D00649:3135..3263,D00650:653..763, FT D00650:1033..1117,D00651:66..227,D00652:55..246,D00653:357 FT ..538,89..232) FT /note="gamma-actin precursor" FT /codon_start!29 FT /db_xref="PID:e34116" FT /translation="PEWPQTASPWIRVVPWGIRRLLRFASMEYTKGKLPIFLAGNGMPVFT GEEADLFDDSVRVNYFNWYINEVLKAVKEDL VDVRSYIVRSLIDGYEGPLGFSQRFGLYFT HVNFNDSSRPRTPRKSAYLFTSIIEKNGFSAKKVKRNPLPVRADFTSRARVTDSLPSEVFT PSK AKISVEKFSKQPRFERDLFYDGRFRDDFLWGVSSSPYQIEGGWNADGKGPSIWDNFFT THTPGNGVKDNATGDVACDSYHQLDADLNILRTLKVKSYRFSISWSRIFPTGRNS TINKFT QGVDYYNRLIDSLVDNNIFPMVTLFHWDLPQALQDIGGWENPSLIELFDSYADYCFKTFFT GDRVKFWMTFNEPWCHVVLGYSSGIFP PSVQEPGWLPYKVSHIVIKAHARVYHTYDEKYFT RSEQKGVISLSLNTHWAEPKDPGLQRDVEAADRMLQFTMGWFAHPIFKNGDYPDVMKWTFT VGNRSELQHLASSRLPTFTEEEKNYVRGTADVFCHNTYTSVFVQHSTPRLNPPSYDDDMFT ELKLIEMNSSTGVMHQDVPWGTRRLLNWIKEEYGNIPIYITENGQGLENPT LDDTERIFFT YHKTYINEALKAYKLDGVDLRGYSAWTLMDDFEWLLGYTMRFGLYYVDFNHVSRPRTARFT ASARYYPDLIANNGMPLAREDEF LYGEFPKGFIWSAASASYQVEGAWRADGKGLSIWDTFT FSHTPLRIGNDDNGDVACDSYHKIAEDVVALQNLGVSHYRFSIAWSRILPDGTTKFINEFT AGLSYYVRFIDALLAAGITPQVTIYHWDLPQALQDVGGWENETIVQRFKEYADVLFQRLFT GDRVKFWITLNEPFVIAAQGYGTGVSAPGISFRPGTAPYIAGHNLIK AHAEAWHLYNDVFT YRARQGGTISITISSDWGEPRDPTNREHVEAARSYVQFMGGWFAHPIFKNGDYPEVMKTFT RIRDRSLGAGLNKSRLPEF TESEKSRIKGTFDFFGFNHNTTVLAYNLDYPAAFSSFDADFT RGVASIADSSWPVSGSFWLKVTPFGFRRILNWLKEEYNNPPIYVTENGVSRRGEPELNDFT TDRIYYLRSYINEALKAVHDKVDLRGYTVWSIMDNFEWATGFAERFGVHFVNRSDPSLPFT RIPRASAKFYATIVRCNGFPDPAQGPHPCLQQPEDAAPTASPV QSEVPFLGLMLGIAEAFT QTALYVLFALLLLGACSLAFLTYNTGRRSKQGNAQPSQHQLSPISSF"

ERROR:

syntax error, at "129 /db_xref="PID:e34116" /translation="PEWPQTASPWIRVVPWGIRRLLRFASMEYTKGKLPIFLAGNGM GENBANK 92 LOCUS HUMACTSG7 466 bp DNA PRI 23-JAN-1992 DEFINITION Human enteric smooth muscle gamma-actin gene, exon 9 and 3' flank. ACCESSION D00654 NID g219424 KEYWORDS actin; gamma-actin. SEGMENT 7 of 7 SOURCE Human peripheral blood genomic DNA, clone HACTSG-112. ORGANISM Homo sapiens Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Mammalia; Theria; Eutheria; Primates; Haplorhini; Catarrhini; Hominidae. REFERENCE 1 (bases 89 to 309) AUTHORS Miwa,T. and Kamada,S. TITLE The nucleotide sequence of a human smooth muscle (enteric type) gamma-actin cDNA JOURNAL Nucleic Acids Res. 18, 4263-4263 (1990) MEDLINE 90332437 REFERENCE 2 (bases 1 to 466) AUTHORS Miwa,T., Manabe,Y., Kurokawa,K., Kamada,S., Kanda,N., Bruns,G., Ueyama,H. and Kakunaga,T. TITLE Structure, chromosome location, and expression of the human smooth muscle (enteric type) gamma-actin gene: evolution of six human actin genes JOURNAL Mol. Cell. Biol. 11, 3296-3306 (1991) MEDLINE 91246198 COMMENT These data kindly submitted in computer readable form by: Takeshi Miwa Department of Oncogene Research Research Institute for Microbial Diseases Osaka University 3-1 Yamadaoka Suita Osaka 565 Japan Phone: 06-875-2470 Fax: 06-875-1292. NCBI gi: 219424 FEATURES Location/Qualifiers 1..466 /organism="Homo sapiens" CDS_pept join(D00649:2129..2254,D00649:3135..3263,D00650:653..763, D00650:1033..1117,D00651:66..227,D00652:55..246, D00653:357..538,89..232) /note="gamma-actin precursor; NCBI gi: 219426" /codon_start=1 /db_xref="PID:g219426" /translation="MCEEETTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGV MVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEH PTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGV THNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLC YVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIH ETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPP ERKYSVWIGGSILASLSTFQQMWISKPEYDEAGPSIVHRKCF" --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50