From owner-embldatabank@net.bio.net Mon Jun 07 23:00:00 1993 Path: biosci!daresbury!mrccrc!gwilliam From: gwilliam@crc.ac.uk (Gary Williams x3294) Newsgroups: bionet.molbio.embldatabank Subject: Warning - amino acid sequence in EMBL pro.dat Keywords: warning Message-ID: <1993Jun8.131546.24238@crc.ac.uk> Date: 8 Jun 93 13:15:46 GMT Sender: news@crc.ac.uk Organization: MRC Human Genome Resource Centre Lines: 48 Nntp-Posting-Host: tin The following sequence occurs in the file 'pro.dat' in EMBL release 35 available from the EMBL FTP server ftp.embl-heidelberg.de in the file /pub/databases/embl/release/pro.dat.Z date-stamped 'June 5 17:14' ID A01448 standard; DNA; PRO; 397 BP. XX AC A01448; XX DT 29-MAR-1993 (Rel. 35, Created) DT 29-MAR-1993 (Rel. 35, Last updated, Version 1) XX DE E.coli tyrB aminotransferase protein sequence XX KW . XX OS Escherichia coli OC Prokaryota; Bacteria; Gracilicutes; Scotobacteria; OC Facultatively anaerobic rods; Enterobacteriaceae; Escherichia. XX RN [1] RA Primrose S.B., Edwards R.M.; RT "The cloning and utilization of aminotransferase genes."; RL Patent number EP0293514-A/2, 07-DEC-1988. RL G.D. Searle & Co.. XX FH Key Location/Qualifiers FH FT source 1..397 FT /organism="Escherichia coli" XX SQ Sequence 397 BP; 51 A; 5 C; 30 G; 15 T; 296 other; vfqkvdayag dpiltlmerf kedprsdkvn lsiglyyned giipqlqava eaearlnaqp 60 hgaslylpme glncyrhaia pllfgadhpv lkqqrvatiq tlggsgalkv gadflkryfp 120 esgvwvsdpt wenhvaifag agfevstypw ydeatngvrf ndllatlktl parsivllhp 180 cchnptgadl tndqwdavie ilkarelipf ldiayqgfga gmeedayair aiasaglpal 240 vsnsfskifs lygervggls vmcedaeaag rvlgqlkatv rrnyssppnf gaqvvaavln 300 dealkaswla eveemrtril amrqelvkvl stempernfd yllnqrgmfs ytglsaaqvd 360 rlreefgvyl iasgrmcvag lntanvqrva kafaavm 397 // -- GARY WILLIAMS, Computing Services, Janet: G.Williams@UK.AC.CRC MRC Human Genome Mapping Project, Internet: G.Williams@CRC.AC.UK Watford Rd, HARROW, Middx, HA1 3UJ, UK ** Sequence databases have ** Tel 081-869 3294 Fax 081-423 1275 ** about a 3% error content ** From owner-embldatabank@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!comp.bioz.unibas.ch From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.announce,bionet.molbio.embldatabank Subject: EMBL database availability Keywords: keeping FTP traffic low Message-ID: <1993Jun9.141817.26005@comp.bioz.unibas.ch> Date: 9 Jun 93 14:18:17 GMT Sender: kristoff@net.bio.net Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 57 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:576 bionet.molbio.embldatabank:183 You might know that we maintain a very large molecular biology database server accessible via FTP, GOPHER, and HASSLE. Periodically, I receive messages like (original quote) > My apologies for ftping some unwanted files. I wanted to get a > copy of the recent embl and pir dbases for running blast. And I realized > I copied some outdated files. > Once again my apologies for the apparent misuse of network > resources. > I would appreciate if you can advise me how I can get the above mentioned > dbases (and the updates) in an acceptable manner. The reason for 'outdated files' is that he EMBL CD-ROM arrives usually a couple of days later than we install the magnetic version in the different formats.I won't describe PIR International Access, but will tell on EMBL databases. Several points to be made here: (1) Computer networks are extremely unsuited for transporting full database releases. Unless there is a well-functioning data distribution schema, ftp'ing databases of this size on transnational lines is not appreciated by the network providers and we (Molecular Biology Users) can ruin our image entirely if all end-users do this in uncoordinated fashion. (2) CD-ROMs are cheap and easy to ship. If you have the demand to get a database not currently present in your portfolio, ask the database providers to ship you the databases you want. (3) If you look for these issues in Europe, the European Molecular Biology network (EMBnet) is the umbrella organisation which keeps copies of the EMBL database in each country, on the so-called 'national node' in Norway, Sweden, Finnland, Denmark, UK, Netherlands, Belgium, France, Germany, Switzerland, Spain, Italy, Greece, Israel. Other nodes are about being started in Portugal, Austria and more coutries. Inquiries welcome! EMBL maintains also an ftp server with their current database, and this archive is mirrored by the Israelian EMBnet node, and also partially on others. (4) If you look for the EMBL database in the US, Mike Cherry volunteered to make the EMBL database available on his machine, anonymous ftp frodo.mgh.harvard.edu, in compressed form. (5) If you look for the _updates_ to the EMBL database, there are sevaral possibilities. (1) The NCBI keeps collaborating with EMBL to incorporate the entries concerned into the GENBANK releases. (2) Mike Cherry mirrors the updates on a weekly basis from Europe. (3) Various national EMBnet nodes provide the data to their community on demand or via ftp archive. -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-embldatabank@net.bio.net Thu Jun 10 23:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.embldatabank Subject: Re: EMBL vs. PIR entries/errors? Message-ID: <01GZ9C3WC8C2A9L0Y9@NBRF.Georgetown.Edu> Date: 11 Jun 93 21:25:54 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 49 In message <9306111647.AA17621@net.bio.net> Roland (rhubner@molbiol.ox.ac.uk) inquires: > 2)lipase 2 of Moraxella appears however in PIR2 under A39556 as well as lipase > 3, but lipase 1 is not there... Do sequences that have been translated (ONLY) > appear in PIR? I thought that only aa sequenced stuff appears > there... > 3)another lipase from Psychrobacter entered correctly EMBL (X67712; > Empro:Pilipaa), but has TWO entries in PIR3: S28225 and S26486!!? Lipase 1, 2 and 3 from Moraxella sp. all appear in PIR. PIR3:S12104 Lipase 1 - Moraxella sp. PIR2:A39556 triacylglycerol lipase (EC 3.1.1.3) 2 - Moraxella sp. TA144 PIR3:S14276 Triacylglycerol lipase (EC 3.1.1.3) - Moraxella sp. (From the title of the article the S14276 entry appears to be a product of the "lip3" gene, and without reading the paper I must assume that is what it probably is.) It would be a very poor database, indeed, if the PIR did not have translated sequences since these days most larger sequences are only available from nucleotide sequence translations. You are perhaps getting this issue confused with the PIR submission policy. The PIR does not accept the _submission_ of peptide sequences determined solely by the translation of nucleotide sequences. The PIR requests authors to submit nucleotide sequences (possibly with translations) to the recognized nucleotide sequence depositories for assignment of nucleotide sequence accession codes. The PIR acquires the entries from the nucleotide sequence depositories, checks the translations and assigns accession codes to the protein sequences with the nucleotide cross-references already made. This policy saves time for the authors (they only have to deal with one database to get a publishable accession number for the proper experimental entity) and for the databases because the correct cross-references can be created without having to do sequence searches. The appearance of both S26486 and S28225 can be explained because of this policy. The entry derived from EMBL submission is S26486. The entry derived from journal scanning is S28225. It occassionally happens (more often than you would think) that the published sequence is not the same as the submitted sequence for the same authors. Just in case, entries are prepared for both. (We would have to do it anyway just to be able to compare them.) Eventually, the entries will be merged and annotated. This all goes especially well when, as in this case, the submitted and published sequence translations are identical. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-embldatabank@net.bio.net Thu Jun 10 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rhubner From: rhubner@molbiol.ox.ac.uk Newsgroups: bionet.molbio.embldatabank Subject: EMBL vs. PIR entries/errors? Message-ID: <1993Jun11.163234.1@molbiol.ox.ac.uk> Date: 11 Jun 93 15:32:34 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 13 Nntp-Posting-Host: heatly Nntp-Posting-User: rhubner Hi group, friends of mine are puzzled with database entries to EMBL and PIR. 1)the entries X53868 and J03545 were attributed for lipase 2 of Moraxella sp. and human pancreatic elastase nucleotide sequences respectively. Where are they? Note that lipase 1 and 3 of Moraxella are in the database under Empro:Mslip3 (X53869) and Empro:Mslipase (X53053)...but the above sequences didn't appear with string searches of different types! 2)lipase 2 of Moraxella appears however in PIR2 under A39556 as well as lipase 3, but lipase 1 is not there... Do sequences that have been translated (ONLY) appear in PIR? I thought that only aa sequenced stuff appears there... 3)another lipase from Psychrobacter entered correctly EMBL (X67712; Empro:Pilipaa), but has TWO entries in PIR3: S28225 and S26486!!? thanks for any comment, Roland From owner-embldatabank@net.bio.net Thu Jun 10 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: Re: Warning - amino acid sequence in EMBL pro.dat Message-ID: <1993Jun9.220045.92012@embl-heidelberg.de> Date: 9 Jun 93 21:00:45 GMT References: <1993Jun8.131546.24238@crc.ac.uk> Organization: EMBL, European Molecular Biology Laboratory Lines: 15 In article <1993Jun8.131546.24238@crc.ac.uk>, gwilliam@crc.ac.uk (Gary Williams x3294) writes: > > The following sequence occurs in the file 'pro.dat' in EMBL release 35 > available from the EMBL FTP server ftp.embl-heidelberg.de in the file > /pub/databases/embl/release/pro.dat.Z date-stamped 'June 5 17:14' >... We apologise for this mistake. It is an amino acid sequence captured from the patent literature which was erroneously flagged as being nucleotide :-( It should not happen again. Regards, Peter Stoehr EMBL Data Library From owner-embldatabank@net.bio.net Fri Jun 11 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.embldatabank Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9306120900.AA28151@net.bio.net> Date: 12 Jun 93 09:00:03 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 143 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** 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. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ ... **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add you name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database will serve as a directory that will enable biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database will be indexed for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data will be available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. (Note as of 5 May 93 - the address database will be updated nightly and will go on-line soon after we have collected and processed the initial rush of data). IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-embldatabank@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!daresbury!cnbvx3.cnb.uam.es!mrege From: mrege@cnbvx3.cnb.uam.es Newsgroups: bionet.molbio.embldatabank Subject: Riders of the lost gene Message-ID: <1993Jun16.134141.47@cnbvx3.cnb.uam.es> Date: 16 Jun 93 13:41:41 GMT Organization: C.N.Biotecnologia, CSIC Lines: 21 Hi, Netters, This is to report an error in the EMBL nucleic acid database. We are looking for the gene and protein sequence of lom, a gene from bacteriophage lambda: Barondess and Beckwith (1990) 'A bacterial virulence determinant encoded by lysogenic coliphage lambda' Nature, 346:871-74. The sequence we retrieved from the database was BLAMLOM X55792, which has found to be the sequence of the gene 'bor', described in the same paper. Searching for 'bor' did not retrieve any sequence, nor lom nor bor. Please, can anyone find for us this sequence, or is it definitively lost in the cyberspace? Thanks, Miquel Regue e-mail:regue@farmacia.ub.es Dept. Microbiology Fac. of Pharmacy University of Barcelona From owner-embldatabank@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.embldatabank Subject: Re: Riders of the lost gene Message-ID: <1993Jun16.144848.642@welchgate.welch.jhu.edu> Date: 16 Jun 93 14:48:48 GMT References: <1993Jun16.134141.47@cnbvx3.cnb.uam.es> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 117 In article <1993Jun16.134141.47@cnbvx3.cnb.uam.es> mrege@cnbvx3.cnb.uam.es writes: >Hi, Netters, > >This is to report an error in the EMBL nucleic acid database. >We are looking for the gene and protein sequence of lom, a gene from >bacteriophage lambda: Barondess and Beckwith (1990) 'A bacterial virulence >determinant encoded by lysogenic coliphage lambda' Nature, 346:871-74. > >The sequence we retrieved from the database was BLAMLOM X55792, which >has found to be the sequence of the gene 'bor', described in the same >paper. Searching for 'bor' did not retrieve any sequence, nor lom nor bor. > >Please, can anyone find for us this sequence, or is it definitively lost >in the cyberspace? > A quick gopher search of EMBL for: lom or bor finds the following two entries. ----------- ID BLAMLOM standard; DNA; PHG; 326 BP. XX AC X55792; XX DT 01-APR-1993 (Rel. 35, Created) DT 01-APR-1993 (Rel. 35, Last updated, Version 1) XX DE Bacteriophage lambda lom gene XX KW envelope protein. XX OS Bacteriophage lambda OC Viridae; ds-DNA nonenveloped viruses; Siphoviridae. XX RN [1] RP 1-326 RA Barondess J.J., Beckwith J.; RT "A bacterial virulence determinant encoded by lysogenic coliphage RT lambda"; RL Nature 346:871-874(1990). XX FH Key Location/Qualifiers FH FT source 1..326 FT /organism="Bacteriophage lambda" FT CDS 24..317 FT /gene="lom" XX SQ Sequence 326 BP; 104 A; 72 C; 69 G; 81 T; 0 other; caaaaagcat cgggaataac accatgaaaa aaatgctact cgctactgcg ctggccctgc 60 ttattacagg atgtgctcaa cagacgttta ctgttcaaaa caaaccggca gcagtagcac 120 caaaggaaac catcacccat catttcttcg tttctggaat tgggcagaag aaaactgtcg 180 atgcagccaa aatttgtggc ggcgcagaaa atgttgttaa aacagaaacc cagcaaacat 240 tcgtaaatgg attgctcggt tttattactt taggcattta tactccgctg gaagcgcgtg 300 tgtattgctc acaataattg catgag 326 // -------------------------- ID BLAMBOR standard; DNA; PHG; 701 BP. XX AC X55793; XX DT 01-APR-1993 (Rel. 35, Created) DT 01-APR-1993 (Rel. 35, Last updated, Version 1) XX DE Bacteriophage lambda bor gene XX KW envelope protein. XX OS Bacteriophage lambda OC Viridae; ds-DNA nonenveloped viruses; Siphoviridae. XX RN [1] RP 1-701 RA Barondess J.J., Beckwith J.; RT "A bacterial virulence determinant encoded by lysogenic coliphage RT lambda"; RL Nature 346:871-874(1990). XX FH Key Location/Qualifiers FH FT source 1..701 FT /organism="Bacteriophage lambda" FT CDS 66..686 FT /gene="bor" XX SQ Sequence 701 BP; 157 A; 144 C; 232 G; 168 T; 0 other; ctgagtgtgt tacagaggtt cgtccgggaa cgggcgtttt attataaaac agtgagaggt 60 gaacgatgcg taatgtgtgt attgccgttg ctgtctttgc cgcacttgcg gtgacagtca 120 ctccggcccg tgcggaaggt ggacatggta cgtttacggt gggctatttt caagtgaaac 180 cgggtacatt gccgtcgttg tcgggcgggg ataccggtgt gagtcatctg aaagggatta 240 acgtgaagta ccgttatgag ctgacggaca gtgtgggggt gatggcttcc ctggggttcg 300 ccgcgtcgaa aaagagcagc acagtgatga ccggggagga tacgtttcac tatgagagcc 360 tgcgtggacg ttatgtgagc gtgatggccg gaccggtttt acaaatcagt aagcaggtca 420 gtgcgtacgc catggccgga gtggctcaca gtcggtggtc cggcagtaca atggattacc 480 gtaagacgga aatcactccc gggtatatga aagagacgac cactgccagg gacgaaagtg 540 caatgcggca tacctcagtg gcgtggagtg caggtataca gattaatccg gcagcgtccg 600 tcgttgttga tattgcttat gaaggctccg gcagtggcga ctggcgtact gacggattca 660 tcgttggggt cggttataaa ttctgattag ccaggtaaca c 701 // Best of luck, Dan Jacobson danj@welchgatee.welch.jhu.edu From owner-embldatabank@net.bio.net Wed Jun 16 23:00:00 1993 Path: biosci!TWNAS886.BITNET!MBDMITRY From: MBDMITRY@TWNAS886.BITNET Newsgroups: bionet.molbio.embldatabank Subject: sequence charon 4a Message-ID: <01GZI32TDQ4K90PSJ1@ccvax.sinica.edu.tw> Date: 18 Jun 93 06:05:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 I would like to receive sequence of lambda charon 4a vector left arm DNA from the position 18560(Kpn1-site) to the position 20660 (Sac1-site of lac5 insert). Thanks very much Dmitry Bessarab Institute of Molecular Biology Academia Sinica Nankang, Taipei,11529 Rep. of China e-mail mbdmitry@ccvax.sinica.edu.tw From owner-embldatabank@net.bio.net Thu Jun 17 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rhubner From: rhubner@molbiol.ox.ac.uk Newsgroups: bionet.molbio.embldatabank Subject: EMBL vs. PIR entries/errors? --continued Message-ID: <1993Jun18.221142.1@molbiol.ox.ac.uk> Date: 18 Jun 93 21:11:42 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 21 Nntp-Posting-Host: heatly Nntp-Posting-User: rhubner Hi again, Thanks for the message. Initially PIR had been searched ONLY for EC number and we therefore missed "unfortunately" lipase 1... Interestingly, I could NOW also find lip2 of Moraxella in EMBL release 35 with a stringsearch for "lip" or "lipase"!!! *** ID MSLIP2 standard; DNA; PRO; 2134 BP. XX AC X53868; XX DT 27-APR-1993 (Rel. 35, Created) DT 27-APR-1993 (Rel. 35, Last updated, Version 2) XX DE Moraxella sp. lip2 gene for lipase 2 *** I think I erred in the elastase (pancreatic) accession number I reported... should be J03516 according to publication... NOT found with stringsearch under elastase and also not with the number [J03517 will give an entry]... Roland From owner-embldatabank@net.bio.net Sun Jun 20 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!ouzounis From: ouzounis@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: GenPept question Message-ID: <1993Jun21.153603.95282@embl-heidelberg.de> Date: 21 Jun 93 14:36:03 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 13 Hi one point for clarification: how is GenPept produced? Only from doc lines in GenBank, or also by some intelligent program for ORF identification?? Thanks... C A Ouzouns EMBL Heidelberg Germany ouzounis@embl-heidelberg.de From owner-embldatabank@net.bio.net Sun Jun 20 23:00:00 1993 Path: biosci!FCRFV2.NCIFCRF.GOV!GUNNELL From: GUNNELL@FCRFV2.NCIFCRF.GOV ("Mark A. Gunnell") Newsgroups: bionet.molbio.embldatabank Subject: RE: GenPept question Message-ID: <930621111751.20209310@FCRFV2.NCIFCRF.GOV> Date: 21 Jun 93 15:17:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 25 C A Ouzouns, EMBL, Heidelberg, asked: > one point for clarification: how is GenPept produced? Only from doc lines > in GenBank, or also by some intelligent program for ORF identification?? The version of GenPept that I distribute from fconvx.ncifcrf.gov is entirely derived from the GenBank "/translation=" feature qualifiers (see 1.4.6 in the GenPept 77.0 release notes). According to the GenBank Release 77.0 release notes, the "/translation=" data is "automatically generated". I can't say whether or not the program used by the NCBI folks is utilizing an ORF identification scheme to generate this information. Would anyone from NCBI like to comment? Best Regards, -Mark Gunnell ------------------------------------------------------------------------------- Mark A. Gunnell | Internet: gunnell@ncifcrf.gov Sci. Applications Analyst | Bitnet: gunnell%ncifcrf.gov@cunyvm.bitnet Biomedical Supercomputer Center | Phone: (301) 846-5779 PRI/DynCorp | NCI-FCRDC | PO Box B, Bldg 430 | Frederick, MD 21702-1201 USA | ------------------------------------------------------------------------------- From owner-embldatabank@net.bio.net Mon Jun 21 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!cs.utexas.edu!uunet!pipex!doc.ic.ac.uk!daresbury!cnbvx3.cnb.uam.es!mrege From: mrege@cnbvx3.cnb.uam.es Newsgroups: bionet.molbio.embldatabank Subject: Re: Riders of the lost gene/THANKS! Message-ID: <1993Jun22.170723.49@cnbvx3.cnb.uam.es> Date: 22 Jun 93 17:07:22 GMT References: <1993Jun16.134141.47@cnbvx3.cnb.uam.es> <1993Jun16.144848.642@welchgate.welch.jhu.edu> Organization: C.N.Biotecnologia, CSIC Lines: 23 Hello, Thank you for your answer and thanks are also given to the people who answered me directly. Now we have got both sequences and after comparing them with the paper they were reported in (Nature, 346:871-874), we have found that their names are, as we figured out, interchanged. So the entry named BLAMLOM corresponds to gene and protein bor, and the one named BLAMBOR is actually the gene and protein lom. Hope this helps to correct the error. Cheers, Miquel ==================================================================== Miquel Regue e-mail: regue@farmacia.ub.es Dept. Microbiology Fac. of Pharmacy University of Barcelona From owner-embldatabank@net.bio.net Mon Jun 21 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Newsgroups: bionet.molbio.embldatabank Subject: Re: GenPept question Message-ID: <1993Jun22.195631.20426@nlm.nih.gov> Date: 22 Jun 93 19:56:31 GMT References: <930621111751.20209310@FCRFV2.NCIFCRF.GOV> Sender: news@nlm.nih.gov Distribution: bionet Organization: National Library of Medicine Lines: 20 X-Newsreader: Tin 1.1 PL4 GUNNELL@FCRFV2.NCIFCRF.GOV (Mark A. Gunnell) writes: : C A Ouzouns, EMBL, Heidelberg, asked: : : > one point for clarification: how is GenPept produced? Only from doc lines : > in GenBank, or also by some intelligent program for ORF identification?? : : The version of GenPept that I distribute from fconvx.ncifcrf.gov is entirely : derived from the GenBank "/translation=" feature qualifiers (see 1.4.6 in the : GenPept 77.0 release notes). According to the GenBank Release 77.0 release : notes, the "/translation=" data is "automatically generated". I can't say : whether or not the program used by the NCBI folks is utilizing an ORF : identification scheme to generate this information. Would anyone from NCBI : like to comment? NCBI is not searching the sequence to add potential coding regions to GenBank -- the author's specification of the coding region (the CDS feature) is used to do the translation. Dennis Benson NCBI From owner-embldatabank@net.bio.net Wed Jun 23 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: On the usefulness of sequences in the databases Keywords: Patents, database quality, trash Message-ID: <1993Jun24.170658.14826@comp.bioz.unibas.ch> Date: 24 Jun 93 17:06:58 GMT Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 45 Xref: biosci bionet.molbio.genbank:1318 bionet.molbio.embldatabank:196 Nntp-Posting-Host: biox.embnet.unibas.ch Colleagues, I have full sympathy in being eager to collect all and everything in the sequence data arena. Therefore, I currently compare GENBANK 77 vs. EMBL 35, and try to figure out the differences. Most can be explained, however, look at the following sequence: LOCUS A00674 6 bp DNA PAT 29-JAN-1993 DEFINITION Nucleotide sequence 3 from patent number WO8601533 ACCESSION A00674 KEYWORDS . SOURCE Unknown ORGANISM Unknown Unclassified. REFERENCE 1 (bases 1 to 6) AUTHORS TITLE 'PRODUCTION OF CHIMERIC ANTIBODIES' JOURNAL Patent: WO 8601533-A 3 13-MAR-1986; STANDARD full automatic BASE COUNT 3 a 2 c 0 g 1 t ORIGIN 1 cactaa I start to worry what the purpose of these sequences is. I am aware of the fact that this is an extreme, but there are a couple of more, very short sequences. In particular, these 'patent' data are of more than doubtful quality. However, as both EMBL and GENBANK incorporate these, I need to explain to my customers what the need is to have a hexanucleotide in a sequence database, which occurs 28340 times in over 70000 sequences? Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-embldatabank@net.bio.net Thu Jun 24 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!darwin.sura.net!lhc!object!ostell From: ostell@object.nlm.nih.gov (Jim Ostell) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Re: On the usefulness of sequences in the databases Message-ID: <1993Jun25.125802.23133@nlm.nih.gov> Date: 25 Jun 93 12:58:02 GMT References: <1993Jun24.170658.14826@comp.bioz.unibas.ch> Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 52 Xref: biosci bionet.molbio.genbank:1322 bionet.molbio.embldatabank:197 X-Newsreader: Tin 1.1 PL4 Patents in the sequence databases: There has been some confusion about the purpose, meaning, and quality of the patent sequences appearing in the sequence databases. To give a little background, the European, U.S., and Japanese Patent Offices have made an agreement to exchange patent related sequences with each other and to make them available to the public. Each office has made their own arrangements for capturing their patent sequence data. In the U.S., the NCBI is working with the U.S. Patent and Trademark Office to enter the backlog of patents, gather the new patents, and to distribute them in GenBank. Speaking now only for the U.S. effort, most of the backlog has been entered. In the last tow releases of GenBank, NCBI has included patent sequences in a separate division of the database, "PAT". The sequences come jointly from the data capture efforts of EMBL for European patents and the NCBI for the U.S. patents. The agreement with the USPTO was to take only DNA sequences at least 10 residues long. Because a patent is a legal, not a scientific, document, it is often difficult or impossible to reliably capture all the information of biological interest such as features or even the organism name. Further, it is often difficult or impossible, except by careful legal scrutiny, to determine what sequence (if any) is claimed to be patented and what is just an "exhibit" or associated information. Finally, the sequences themselves may be presented in a sufficiently complex manner that it can be hard to determine what the sequence itself is in some regions. In consultation with USPTO then, it became clear that patent sequences could not be guaranteed to be a source of new biological data. We took the approach instead that the purpose of the patent sequences was to serve as a search key back to the original patent. To achieve this, we entered all sequences in the patent which met the length limits and associated them with the patent document. No attempt was made to biologically annotate them or determine what was claimed by the patent. Their most valuable use is to search by sequence similarity to discover patents that may overlap with a possible claim made on a new sequence. The other use would be to find the sequences relevant to a given patent. Since these uses are so specialized, we felt it was important to keep these sequences in a separate division. Note that it is typical for a patent to refer to published sequences or for sequence data to be published after a patent is awarded. So most of these sequences have cognates in the usual divisions of the database. As the sequences directly submitted electronically to USPTO as part of the patent application process become available, it is possible that they will be more fully annotated biologically by the submittor. However, since the immediate submittor is usually a lawyer's office and since such annotation is not required for the patent to be considered, do not expect too much. We hope this clarifies the attributes of patented sequence entries. Jim Ostell NCBI From owner-embldatabank@net.bio.net Sun Jun 27 23:00:00 1993 Path: biosci!ACS.UCALGARY.CA!sjszarka From: sjszarka@ACS.UCALGARY.CA (Steve Szarka) Newsgroups: bionet.molbio.embldatabank Subject: PCR sequences in Databases? Message-ID: <9306280258.AA22023@acs4.acs.ucalgary.ca> Date: 28 Jun 93 02:58:31 GMT Sender: daemon@net.bio.net Reply-To: sjszarka@acs.ucalgary.ca Distribution: bionet Lines: 13 What is the present policy on submitting DNA sequences off of PCR products to the EMBL or Genbank databases? I looked through the Authorin v3.0 program and could not find a PCR heading for the type of molecule sequenced. Is PCR fidelity not reliable enough to include sequence information in the databases? Thanks Steve sjszarka@acs.ucalgary.ca From owner-embldatabank@net.bio.net Sun Jun 27 23:00:00 1993 Path: biosci!ACS.UCALGARY.CA!sjszarka From: sjszarka@ACS.UCALGARY.CA (Steve Szarka) Newsgroups: bionet.molbio.embldatabank Subject: Sequences from PCR fragments in Databases? Message-ID: <9306281825.AA57346@acs4.acs.ucalgary.ca> Date: 28 Jun 93 18:25:25 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 What is the present policy on submitting DNA sequences off of PCR products to the EMBL or Genbank databases? I looked through the Authorin v3.0 program and could not find a PCR heading for the type of molecule sequenced. Is PCR fidelity not reliable enough to include sequence information in the databases? Thanks Steve sjszarka@acs.ucalgary.ca From owner-embldatabank@net.bio.net Mon Jun 28 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!mcsun!news.funet.fi!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Re: On the usefulness of sequences in the databases Message-ID: <1993Jun29.123212.18851@nic.funet.fi> Date: 29 Jun 93 12:32:12 GMT References: <1993Jun24.170658.14826@comp.bioz.unibas.ch> <1993Jun25.125802.23133@nlm.nih.gov> Sender: usenet@nic.funet.fi Organization: Finnish Academic and Research Network Project - FUNET Lines: 70 Xref: biosci bionet.molbio.genbank:1324 bionet.molbio.embldatabank:200 Nntp-Posting-Host: convex.csc.fi In <1993Jun25.125802.23133@nlm.nih.gov> ostell@object.nlm.nih.gov (Jim Ostell) writes: >Patents in the sequence databases: When I was in the States Brewster Kahle said that one of the most popular wais sources was the patent-sampler.src which covered about 2 weeks of Patent applications (18MBytes) from the US Patent Office. Last week when I was at EMBL, Peter Stoehr showed me the patent.dat that is available from the epo (European Patent office), and I thought it might be a good idea to make a wais source from the data. This is a copy of the epo.src ------------------8< --------- clip-------------8<--------- (:source :version 3 :ip-address "128.214.6.100" :ip-name "wais.funet.fi" :tcp-port 210 :database-name "embnet/epo" :cost 0.00 :cost-unit :free :maintainer "harper@wais.funet.fi" :description "Server created with WAIS release 8 b5 on Jun 28 13:47:08 1993 by harper@wais.funet.fi This is a wais source of the genetic material in the European Patent office. The files of type catalog used in the index were: /pub/sci/molbio/databases/patent/patent.dat " ) ------------------8< --------- clip-------------8<--------- If you do not have Xwais for seaching I have also included the epo.src on the gopher at CSC under the directory (WAIS WORLD for the biologist) (That's near enough to WAYNE'S WORLD... isn't it Daniel) WAIS WORLD for the Biologist 1. Agriculture/ 2. Journal TOC search 3. Materials & Methods search 4. Prosite protein database search 5. Search Specialised Databases at Welchlab / 6. Search Usenet News "sci"-groups (UK) 7. Search for Software at EMBL (Mac, Dos, Unix, Vax)/ 8. Search for Software at Indiana - IUBio (Mac, Dos, Unix, Vax)/ 9. Search the Biosci/Bionet newsgroups (USA) --> 10. Search the European Patent Office database (Finland) 11. Search the GDB database (USA) 12. Search the INFO-GCG mailing list (FINLAND) 13. Search the Protein Data Bank (USA) 14. Search the WAIS directory of servers (USA) So now all those commercial firms that have just patented a 10 base pair sequence can now quickly check and see if some-one has already beat them to it:-) RGDS -=ROB=- -- Rob Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-embldatabank@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!sdd.hp.com!cs.utexas.edu!uunet!mcsun!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rhubner From: rhubner@molbiol.ox.ac.uk Newsgroups: bionet.molbio.embldatabank Subject: secondary accession numbers Message-ID: <1993Jul1.234108.1@molbiol.ox.ac.uk> Date: 1 Jul 93 22:41:08 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 11 Nntp-Posting-Host: heatly Nntp-Posting-User: rhubner Hi there group, just to tell to those who aren't aware: sequence entries (e.g. my recent enquiry about a nucleotide sequence for human pancreatic elastase J03516) may represent *secondary* accession numbers and can not be searched for by FETCH (and especially STRINGSEARCH; only ref fields) in GCG. This was the reason why I could not locate the correct entry for this sequence[however,this case is peculiar as there seems to be several entries for J03516 as secondary number]. The SRS software can do the job properly... Special thanks to Kate Rice (EMBL - Heidelberg) to have pointed out these details to me!!! Roland