From owner-bio-srs@hgmp.mrc.ac.uk Mon Jul 8 09:56:38 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 2A1EB17B05 for ; Mon, 8 Jul 2002 09:56:37 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9553017B17 for ; Mon, 8 Jul 2002 09:56:32 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 5571E17B25; Mon, 8 Jul 2002 09:55:41 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C793B17BB4 for ; Sat, 29 Jun 2002 18:04:37 +0100 (BST) Received: from newsmaster1.prod.itd.earthlink.net (newsmaster1.news.pas.earthlink.net [207.217.77.50]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 907D217A7B for ; Sat, 29 Jun 2002 18:04:35 +0100 (BST) Received: from newsread2.prod.itd.earthlink.net (newsread2.pvt [10.4.2.52]) by newsmaster1.prod.itd.earthlink.net (8.8.8+Sun/8.8.8) with ESMTP id KAA18477 for ; Sat, 29 Jun 2002 10:04:34 -0700 (PDT) Received: (from news@localhost) by newsread2.prod.itd.earthlink.net (8.8.7/8.8.5) id KAA06467; Sat, 29 Jun 2002 10:04:33 -0700 (PDT) To: bionet-software-srs@net.bio.net Reply-To: "Peter Markstein" From: "Peter Markstein" Newsgroups: bionet.software.srs Subject: Bioinformatics Conference X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Message-ID: X-Complaints-To: abuse@earthlink.net X-Trace: newsread2.prod.itd.earthlink.net 1025370273 158.252.216.161 (Sat, 29 Jun 2002 10:04:33 PDT) NNTP-Posting-Date: Sat, 29 Jun 2002 10:04:33 PDT Organization: EarthLink Inc. -- http://www.EarthLink.net Date: Mon, 8 Jul 2002 09:55:41 +0100 (BST) X-Razor-id: 8cf5a4fa5520d11a53d6320de3c3f37372a1d060 Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear Colleague, We would like to remind to take advantage of early registration discounts for the first IEEE Computer Society Bioinformatics conference and tutorials at Stanford University, August 14-16, 2002. Visit our web site for the final program and online registration http://conferences.computer.org/bioinformatics We would be happy to send you a hard copy of the final program. Please email your postal address and number of copies needed to bioinformatics@computer.org We are looking forward to seeing you at the conference. The CSB2002 Conference Committee From owner-bio-srs@hgmp.mrc.ac.uk Tue Jul 9 10:05:00 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id C232E17B76 for ; Tue, 9 Jul 2002 10:04:58 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 648E017B7E for ; Tue, 9 Jul 2002 10:04:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id B5D7117BA5; Tue, 9 Jul 2002 09:59:36 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B3EA317AEA for ; Mon, 8 Jul 2002 15:10:52 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id D35E317B11; Mon, 8 Jul 2002 15:10:21 +0100 (BST) To: bionet-software-srs@net.bio.net From: Elisabeth.Gasteiger@isb-sib.ch (Elisabeth Gasteiger) Newsgroups: bionet.software.srs Subject: RE: database cross-reference Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <3D299CB1.2A130E68@isb-sib.ch> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2DC8217AE5 for ; Mon, 8 Jul 2002 15:10:12 +0100 (BST) X-Received: from expasy-ng.isb-sib.ch (expasy-f.unige.ch [192.33.215.142]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7D42B17A56 for ; Mon, 8 Jul 2002 15:09:23 +0100 (BST) X-Received: from isb-sib.ch ([192.33.215.130]) (authenticated bits=0) by expasy-ng.isb-sib.ch (8.12.3/8.12.0) with ESMTP id g68E9HGn020244 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Mon, 8 Jul 2002 16:09:17 +0200 X-Reply-To: Elisabeth.Gasteiger@isb-sib.ch X-Mailer: Mozilla 4.77 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en X-To: bio-srs@net.bio.net X-Cc: hcwang@science.uottawa.ca Date: Tue, 9 Jul 2002 09:59:36 +0100 (BST) X-Razor-id: 80c6b9a808561ecfa46a1a82f6f2d75642d5ad71 Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear Huaichun, > Sir, > for each protein sequence entry in swall, there is a database > cross-reference to EMBL entries (the line begining with > "DR EMBL;". Actually, this is not true for all entries in SWALL (SWISS-PROT, TrEMBL, TrEMBL_new) - there are also entries describing sequences that have been determined on amino acid level only. In those cases there is no link to the nucleotide sequence database. Example: http://us.expasy.org/cgi-bin/niceprot.pl?P29361 > My question is when there are several > cross-refered EMBL entries for one swissprot entry, what > is the difference between these entries; Do the nucleotide entries > have the same sequences? No, not necessarily. One of the primary goals of SWISS-PROT is to be non-redundant, e.g. to have one SWISS-PROT entry per gene, even if there are several sequencing reports in the DNA databases. Some of these underlying EMBL entries may have identical sequences, others only refer to fragments, to one or several exons, and there may be sequencing conflicts or polymorphisms. See the SWISS-PROT user manual, http://www.expasy.org/sprot/userman.html#whatis > > b) Minimal redundancy > > Many sequence databases contain, for a given protein sequence, separate > entries which correspond to different literature reports. In SWISS-PROT we try > as much as possible to merge all these data so as to minimize the redundancy > of the database. If conflicts exist between various sequencing reports, they are > indicated in the feature table of the corresponding entry. If you look at the feature table of TAP1_HUMAN http://us.expasy.org/cgi-bin/niceprot.pl?tAP1_HUMAN#features you will see several variants: FT VARIANT 333 333 I -> V (IN TAP1*02011/PSF1B, FT TAP1*0301/PSF1C, TAP1*0401 AND TAP1*X). FT /FTId=VAR_000092. FT VARIANT 370 370 A -> V (IN TAP1*X). FT /FTId=VAR_013151. FT VARIANT 458 458 V -> L (IN TAP1*0401). FT /FTId=VAR_013152. FT VARIANT 518 518 V -> I (IN TAP1*X). FT /FTId=VAR_013153. FT VARIANT 637 637 D -> G (IN TAP1*02011/PSF1B, TAP1*0401 FT AND TAP1*X). FT /FTId=VAR_000093. FT VARIANT 648 648 R -> Q (IN TAP1*0401). FT /FTId=VAR_013154. FT VARIANT 659 659 R -> Q (IN A LUNG CANCER CELL LINE FT DEFICIENT IN MHC CLASS I PRESENTATION). FT /FTId=VAR_013173. > > For example, when I used SRS to search for TAP1_HUMAN in swall, I got > a protein sequence entry. There are 10 EMBL entries cross-refered > to this protein. They are: > DR EMBL; X66401; CAA47025.1; -. > DR EMBL; X57521; CAA40740.1; -. > DR EMBL; X57522; CAA40741.1; ALT_INIT. > DR EMBL; L21204; AAC12902.1; -. > DR EMBL; L21205; AAC12903.1; -. > DR EMBL; L21206; AAC12904.1; -. > DR EMBL; L21207; AAC12905.1; -. > DR EMBL; L21208; AAC12906.1; -. > DR EMBL; X87344; CAA60785.1; -. > DR EMBL; S70274; AAD14056.1; -. > > What are the same and difference among these 10 EMBL entries? You can use SRS (e.g. srs.ebi.ac.uk) to retrieve those 10 entries from EMBL Accession number: X66401|X57521|..... and then launch clustalw to perform a multiple alignment of all 10 sequences (see below). I hope this helps. Best regards Elisabeth Gasteiger SEVMHC ------------------------------------------------------------ HSMHCAPG ------------------------------------------------------------ HSRING4 GCGGCCGCTTTCGATTTCGCTTTCCCCTAAATGGCTGAGCTTCTCGCCAGCGCAGGATCA HSTAP1A ------------------------------------------------------------ HSTAP1B ------------------------------------------------------------ HSTAP1C ------------------------------------------------------------ HSTAP1D ------------------------------------------------------------ HSTAP1E ------------------------------------------------------------ HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC ---GATCAGGCTCTTTCTCTCTGTAAACCTGCTCCCATGGCATTCTTTTCTGCTTCAATT HSMHCAPG ------------------------------------------------------------ HSRING4 GCCTGTTCCTGGGACTTTCCGAGAGCCCCGCCCTCGTTCCCTCCCCCAGCCGCCAGTAGG HSTAP1A ------------------------------------------------------------ HSTAP1B ------------------------------------------------------------ HSTAP1C ------------------------------------------------------------ HSTAP1D ------------------------------------------------------------ HSTAP1E ------------------------------------------------------------ HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC CAGTCCATCCCTGACCACCCACCCAGCCACCCATGCTGGAAATCTGAGATATCTTTGACT HSMHCAPG ------------------------------------------------------------ HSRING4 GGAGGACTCGGCGGTACCCGGAGCTTCAGGCCCCACCGGGGCGCGGAGAGTCCCAGACCC HSTAP1A ------------------------------------------------------------ HSTAP1B ------------------------------------------------------------ HSTAP1C ------------------------------------------------------------ HSTAP1D ------------------------------------------------------------ HSTAP1E ------------------------------------------------------------ HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC CCTCCACCTTCCCACTCCCACAGCTAATCAGTAGCCAAACCCTTTAGATTCTACTTCCTA HSMHCAPG -------------------------------TCGACGGGATCACGAGGTCAGGAGATCGA HSRING4 GGCCGGGACCGGGACGGCGTCCGAGTGCCAATGGCTAG-CTCTAGGTGTCCCGCTCCCCG HSTAP1A ------------------------------ATGGCTAG-CTCTAGGTGTCCCGCTCCCCG HSTAP1B ------------------------------ATGGCTAG-CTCTAGGTGTCCCGCTCCCCG HSTAP1C ------------------------------ATGGCTAG-CTCTAGGTGTCCCGCTCCCCG HSTAP1D ------------------------------ATGGCTAG-CTCTAGGTGTCCCGCTCCCCG HSTAP1E ------------------------------ATGGCTAG-CTCTAGGTGTCCCGCTCCCCG HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC ATTATCTTGATATTCTATCTCCTCTGCCTCCTCTAATTATGACTTAATTCAGGCTCTTAT HSMHCAPG GA------------CCATCCTGACTACCACGGTGAA------------------------ HSRING4 --------------CGGGTGCCGCTGCCTCCCCGGA----------------GCT----- HSTAP1A --------------CGGGTGCCGCTGCCTCCCCGGA----------------GCT----- HSTAP1B --------------CGGGTGCCGCTGCCTCCCCGGA----------------GCT----- HSTAP1C --------------CGGGTGCCGCTGCCTCCCCGGA----------------GCT----- HSTAP1D --------------CGGGTGCCGCTGCCTCCCCGGA----------------GCT----- HSTAP1E --------------CGGGTGCCGCTGCCTCCCCGGA----------------GCT----- HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC TATCTGTCATTTAAATTATTGCTGTATTGCTACAGGAGTGGTGTGTATATGTGCAACTGT HSMHCAPG --ACCCCGTCTCTACTAAAAAAAATACAAAAAA--------------------------- HSRING4 --TCTCTCGCATGGCTGGGGACAGTACTGCTAC--------------------------- HSTAP1A --TCTCTCGCATGGCTGGGGACAGTACTGCTAC--------------------------- HSTAP1B --TCTCTCGCATGGCTGGGGACAGTACTGCTAC--------------------------- HSTAP1C --TCTCTCGCATGGCTGGGGACAGTACTGCTAC--------------------------- HSTAP1D --TCTCTCGCATGGCTGGGGACAGTACTGCTAC--------------------------- HSTAP1E --TCTCTCGCATGGCTGGGGACAGTACTGCTAC--------------------------- HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC TCATCTTGGTATGCTATAGACTCTTGCCCAGCAGTTTTGCCTCAATTCTTTAAAAGCTCC HSMHCAPG ----------------------CTAGCCAGG---------CATGGTGGC----------- HSRING4 --------------------TTCTCGCCGA----------CTGGGTGCT------GCTCC HSTAP1A --------------------TTCTCGCCGA----------CTGGGTGCT------GCTCC HSTAP1B --------------------TTCTCGCCGA----------CTGGGTGCT------GCTCC HSTAP1C --------------------TTCTCGCCGA----------CTGGGTGCT------GCTCC HSTAP1D --------------------TTCTCGCCGA----------CTGGGTGCT------GCTCC HSTAP1E --------------------TTCTCGCCGA----------CTGGGTGCT------GCTCC HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC AGTTCATTGTTTGAAATATCAATCAGAACATTTTTTCCAAAATGCTAAAATGATTGTCAT HSMHCAPG -GGGCGCC--------TGTAGTTCCAGCTACT---------------------------- HSRING4 GGACCGC----------GCTGCCCCGCATATTCTCCCTG--------------------- HSTAP1A GGACCGC----------GCTGCCCCGCATATTCTCCCTG--------------------- HSTAP1B GGACCGC----------GCTGCCCCGCATATTCTCCCTG--------------------- HSTAP1C GGACCGC----------GCTGCCCCGCATATTCTCCCTG--------------------- HSTAP1D GGACCGC----------GCTGCCCCGCATATTCTCCCTG--------------------- HSTAP1E GGACCGC----------GCTGCCCCGCATATTCTCCCTG--------------------- HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC TCCCCAGTTTTAATATCTCTATCATCTGCTAAGTAAAAGCAAGCTCCTCCTTGTGGCGTA HSMHCAPG ---CGGGAGGCTGAGGAGGGAGAA--TGGCGTGAA------------CCCGGGAGGCGGA HSRING4 ---CTGGTGCCCACCGCGCTGCCA-CTGCTCCGGG------------TCTGGGCGGTGGG HSTAP1A ---CTGGTGCCCACCGCGCTGCCA-CTGCTCCGGG------------TCTGGGCGGTGGG HSTAP1B ---CTGGTGCCCACCGCGCTGCCA-CTGCTCCGGG------------TCTGGGCGGTGGG HSTAP1C ---CTGGTGCCCACCGCGCTGCCA-CTGCTCCGGG------------TCTGGGCGGTGGG HSTAP1D ---CTGGTGCCCACCGCGCTGCCA-CTGCTCCGGG------------TCTGGGCGGTGGG HSTAP1E ---CTGGTGCCCACCGCGCTGCCA-CTGCTCCGGG------------TCTGGGCGGTGGG HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC GCAGGGCCCACGTGATCTGGCCCTTGCCCGAATTTGTAGCTTATCACAACATCCTTCTAC HSMHCAPG GCTT-GCAG--------TGAGCCGAGATTGTGCCACTGCACTCCAGCCTGGGCGACAGAG HSRING4 CCTGAGCCG-------CTGGGCCGTGCTCTGGCTGGGGGCCTG---CGGGGTCCTCAGGG HSTAP1A CCTGAGCCG-------CTGGGCCGTGCTCTGGCTGGGGGCCTG---CGGGGTCCTCAGGG HSTAP1B CCTGAGCCG-------CTGGGCCGTGCTCTGGCTGGGGGCCTG---CGGGGTCCTCAGGG HSTAP1C CCTGAGCCG-------CTGGGCCGTGCTCTGGCTGGGGGCCTG---CGGGGTCCTCAGGG HSTAP1D CCTGAGCCG-------CTGGGCCGTGCTCTGGCTGGGGGCCTG---CGGGGTCCTCAGGG HSTAP1E CCTGAGCCG-------CTGGGCCGTGCTCTGGCTGGGGGCCTG---CGGGGTCCTCAGGG HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC CCCCCATTACCTCCTATTATACAGGAACACCCAAGCGACCTTCACAACATTCATATCAAC HSMHCAPG CGAGACTCCGTCTCAAAAAAAAAAAAAAAA------------------------------ HSRING4 CAACGGTTGGCTCC--------AAGAGCG------------------------------- HSTAP1A CAACGGTTGGCTCC--------AAGAGCG------------------------------- HSTAP1B CAACGGTTGGCTCC--------AAGAGCG------------------------------- HSTAP1C CAACGGTTGGCTCC--------AAGAGCG------------------------------- HSTAP1D CAACGGTTGGCTCC--------AAGAGCG------------------------------- HSTAP1E CAACGGTTGGCTCC--------AAGAGCG------------------------------- HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC TAGTACACAGGGTCTCCAAAGAGGACCTCTGGATGCCTGTGATCTTTGTACTTCTGC-CT HSMHCAPG -AAAAAAAAAAAAAAAAAAAAAAAGA----AAAGGATTGTAAG--AGTTACTGTTACATT HSRING4 -AAAACGCAGG-TGCCCAGGGCTGGC---TGGCTGCTTTGAAGCCATTAGCTGCGGCACT HSTAP1A -AAAACGCAGG-TGCCCAGGGCTGGC---TGGCTGCTTTGAAGCCATTAGCTGCGGCACT HSTAP1B -AAAACGCAGG-TGCCCAGGGCTGGC---TGGCTGCTTTGAAGCCATTAGCTGCGGCACT HSTAP1C -AAAACGCAGG-TGCCCAGGGCTGGC---TGGCTGCTTTGAAGCCATTAGCTGCGGCACT HSTAP1D -AAAACGCAGG-TGCCCAGGGCTGGC---TGGCTGCTTTGAAGCCATTAGCTGCGGCACT HSTAP1E -AAAACGCAGG-TGCCCAGGGCTGGC---TGGCTGCTTTGAAGCCATTAGCTGCGGCACT HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC ACCCTTTGCCCTGGCGTGTTTTTCTCTTCCTTCATGTTCTGCTGGCCAAATTGTTTTTCC HSMHCAPG ---TTCTGGCCTAC-------TACCTT--------------------------------- HSRING4 GGGCTTGGCCCTGCCGGGACTTGCCTT--------------------------------- HSTAP1A GGGCTTGGCCCTGCCGGGACTTGCCTT--------------------------------- HSTAP1B GGGCTTGGCCCTGCCGGGACTTGCCTT--------------------------------- HSTAP1C GGGCTTGGCCCTGCCGGGACTTGCCTT--------------------------------- HSTAP1D GGGCTTGGCCCTGCCGGGACTTGCCTT--------------------------------- HSTAP1E GGGCTTGGCCCTGCCGGGACTTGCCTT--------------------------------- HSY3 ------------------------------------------------------------ S70274 ------------------------------------------------------------ HSEVMHC TTCAAGTCTTAGGAGCCTGCCTGATTATGTTCCTCCTATTCCGCATCCTCATAAAATTAC HSMHCAPG ---------TAAAA----TTCCTGTTGCATTTCTTTGTATTTACAA-------------- HSRING4 -----GTTCCGAGAGCTGATCTCATGGGGAGCCCCCGGGTCCGC---------------- HSTAP1A -----GTTCCGAGAGCTGATCTCATGGGGAGCCCCCGGGTCCGC---------------- HSTAP1B -----GTTCCGAGAGCTGATCTCATGGGGAGCCCCCGGGTCCGC---------------- HSTAP1C -----GTTCCGAGAGCTGATCTCATGGGGAGCCCCCGGGTCCGC---------------- HSTAP1D -----GTTCCGAGAGCTGATCTCATGGGGAGCCCCCGGGTCCGC---------------- HSTAP1E -----GTTCCGAGAGCTGATCTCATGGGGAGCCCCCGGGTCCGC---------------- HSY3 ------------------------------------GGGTCCGC---------------- S70274 ------------------------------------------------------------ HSEVMHC TGCGACTTCCAAAACACTTGGCACATTCTTATTTGAATACATTACATTGTTGTGTAATTA HSMHCAPG ----------------------------------GGAAA--------------------- HSRING4 ----------------------------------GGATA--------------------- HSTAP1A ----------------------------------GGATA--------------------- HSTAP1B ----------------------------------GGATA--------------------- HSTAP1C ----------------------------------GGATA--------------------- HSTAP1D ----------------------------------GGATA--------------------- HSTAP1E ----------------------------------GGATA--------------------- HSY3 ----------------------------------GGATA--------------------- S70274 ------------------------------------------------------------ HSEVMHC TCCCTTGGCCCCCTCCCCCAGCACTAGACTCTAAGCTCTTTGAAGGCAGACTATGCCTAT HSMHCAPG --------------------AGACTGAACT--------------------TT-------- HSRING4 --------------------GCACCAGGCT-------------------ACT-------- HSTAP1A --------------------GCACCAGGCT-------------------ACT-------- HSTAP1B --------------------GCACCAGGCT-------------------ACT-------- HSTAP1C --------------------GCACCAGGCT-------------------ACT-------- HSTAP1D --------------------GCACCAGGCT-------------------ACT-------- HSTAP1E --------------------GCACCAGGCT-------------------ACT-------- HSY3 --------------------GCACCAGGCT-------------------ACT-------- S70274 ------------------------------------------------------------ HSEVMHC TCATCTTTGTATTTCTAGCCCTGGGCCCAACACCCAGAATTTCTTGTATTTTCAATATAT HSMHCAPG ------------------TTCTCATCAAAACTAGCT-------TTTTTCTCACAGGTTAA HSRING4 -----------------GCACTGGGGAAGTCACCCT--ACCGCCTTCGTTGTCAGT-TAT HSTAP1A -----------------GCACTGGGGAAGTCACCCT--ACCGCCTTCGTTGTCAGT-TAT HSTAP1B -----------------GCACTGGGGAAGTCACCCT--ACCGCCTTCGTTGTCAGT-TAT HSTAP1C -----------------GCACTGGGGAAGTCACCCT--ACCGCCTTCGTTGTCAGT-TAT HSTAP1D -----------------GCACTGGGGAAGTCACCCT--ACCGCCTTCGTTGTCAGT-TAT HSTAP1E -----------------GCACTGGGGAAGTCACCCT--ACCGCCTTCGTTGTCAGT-TAT HSY3 -----------------GCACTGGGGAAGTCACCCT--ACCGCCTTCGTTGTCAGT-TAT S70274 ------------------------------------------------------------ HSEVMHC GTCTGCCAAATGAATTAGAGCTAATGCCTGAAGGAGAATAAGTTTTTTTGAGAAAGAGGA HSMHCAPG ACTT-------------GCACCAATGTCTGC----------------------------- HSRING4 GC--------------AGCGGCACTGCCCGCAGCAG------------------------ HSTAP1A GC--------------AGCGGCACTGCCCGCAGCAG------------------------ HSTAP1B GC--------------AGCGGCACTGCCCGCAGCAG------------------------ HSTAP1C GC--------------AGCGGCACTGCCCGCAGCAG------------------------ HSTAP1D GC--------------AGCGGCACTGCCCGCAGCAG------------------------ HSTAP1E GC--------------AGCGGCACTGCCCGCAGCAG------------------------ HSY3 GC--------------AGCGGCACTGCCCGCAGCAG------------------------ S70274 ------------------------------------------------------------ HSEVMHC AGAGCCAGGAGGGAGGAGAAGGCAGGGTCCGAAGAGCCCTGGGGGTTTA-CTTGGGGAAG HSMHCAPG ------------------------------------TCTTTTTTTTTAATGTTTTTGGTA HSRING4 ------------------------------------CCCTGTGGCACAA-ACTCGGGAGC HSTAP1A ------------------------------------CCCTGTGGCACAA-ACTCGGGAGC HSTAP1B ------------------------------------CCCTGTGGCACAA-ACTCGGGAGC HSTAP1C ------------------------------------CCCTGTGGCACAA-ACTCGGGAGC HSTAP1D ------------------------------------CCCTGTGGCACAA-ACTCGGGAGC HSTAP1E ------------------------------------CCCTGTGGCACAA-ACTCGGGAGC HSY3 ------------------------------------CCCTGTGGCACAA-ACTCGGGAGC S70274 ------------------------------------------------------------ HSEVMHC ATGCGGTTCCCCATTGCAGCATTCTGCCAGGAGGTGGCACTGCTCTGAAGAGCCAGCTGG HSMHCAPG CTCTGGGCAGACTTCAG-----TTTTTTAAAAAA-----------TAAAGATTCTA-ATG HSRING4 CTCTGGGTGCCCGGCG---------GTCAGGGCG-------GCTCTGGAAACCCTGTGCG HSTAP1A CTCTGGGTGCCCGGCG---------GTCAGGGCG-------GCTCTGGAAACCCTGTGCG HSTAP1B CTCTGGGTGCCCGGCG---------GTCAGGGCG-------GCTCTGGAAACCCTGTGCG HSTAP1C CTCTGGGTGCCCGGCG---------GTCAGGGCG-------GCTCTGGAAACCCTGTGCG HSTAP1D CTCTGGGTGCCCGGCG---------GTCAGGGCG-------GCTCTGGAAACCCTGTGCG HSTAP1E CTCTGGGTGCCCGGCG---------GTCAGGGCG-------GCTCTGGAAACCCTGTGCG HSY3 CTCTGGGTGCCCGGCG---------GTCAGGGCG-------GCTCTGGAAACCCTGTGCG S70274 ------------------------------------------------------------ HSEVMHC TCG-CTTACAGACTGAGGCTGACAGCTTGAAACCAAAGAGGGAACTCCACCAGGAAGCAA HSMHCAPG CAGCTATCTTGGCAT------------TCCCTTTAAATAC------CTGTC--------- HSRING4 TCGGCTTCTAGGCTG----------CCTGGGCTCGGAGACG---CGCCGCC--------- HSTAP1A TCGGCTTCTAGGCTG----------CCTGGGCTCGGAGACG---CGCCGCC--------- HSTAP1B TCGGCTTCTAGGCTG----------CCTGGGCTCGGAGACG---CGCCGCC--------- HSTAP1C TCGGCTTCTAGGCTG----------CCTGGGCTCGGAGACG---CGCCGCC--------- HSTAP1D TCGGCTTCTAGGCTG----------CCTGGGCTCGGAGACG---CGCCGCC--------- HSTAP1E TCGGCTTCTAGGCTG----------CCTGGGCTCGGAGACG---CGCCGCC--------- HSY3 TCGGCTTCTAGGCTG----------CCTGGGCTCGGAGACG---CGCCGCC--------- S70274 ------------------------------------------------------------ HSEVMHC CATTCCTCCACTGGGCTTCCCAGCCCAGTTACATGCCATACTCTGCCCTGGTCAAACAGC HSMHCAPG ------TTAAC-----CTCCTACTTTTATT-----TCCTACTCCTTTCCACACACATGCA HSRING4 -----TCTCGCTG---TTCCTGGTCCTGGTG---GTCCTCTCCTCTCTTGGGGAGATGGC HSTAP1A -----TCTCGCTG---TTCCTGGTCCTGGTG---GTCCTCTCCTCTCTTGGGGAGATGGC HSTAP1B -----TCTCGCTG---TTCCTGGTCCTGGTG---GTCCTCTCCTCTCTTGGGGAGATGGC HSTAP1C -----TCTCGCTG---TTCCTGGTCCTGGTG---GTCCTCTCCTCTCTTGGGGAGATGGC HSTAP1D -----TCTCGCTG---TTCCTGGTCCTGGTG---GTCCTCTCCTCTCTTGGGGAGATGGC HSTAP1E -----TCTCGCTG---TTCCTGGTCCTGGTG---GTCCTCTCCTCTCTTGGGGAGATGGC HSY3 -----TCTCGCTG---TTCCTGGTCCTGGTG---GTCCTCTCCTCTCTTGGGGAGATGGC S70274 ------------------------------------------------------------ HSEVMHC CAAGTCTTCAGGAGGTTACTGGCCCCAGGCGTCTCCCCAGTGACTGATGATGTTAAACCC HSMHCAPG -- ----------------------------------------------------------------- Elisabeth Gasteiger Swiss Institute of Bioinformatics CMU - 1, rue Michel Servet Tel. (+41 22) 702 58 75 CH - 1211 Geneva 4 Switzerland Fax (+41 22) 702 58 58 Elisabeth.Gasteiger@isb-sib.ch http://www.expasy.org/ ----------------------------------------------------------------- --- From owner-bio-srs@hgmp.mrc.ac.uk Thu Jul 11 11:28:44 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id DB8D317B35 for ; Thu, 11 Jul 2002 11:28:41 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C3A3517B30 for ; Thu, 11 Jul 2002 11:28:37 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 3A9E617AA3; Thu, 11 Jul 2002 11:28:21 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A564717B59 for ; Tue, 9 Jul 2002 16:50:52 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id C0D7C17B31; Tue, 9 Jul 2002 16:50:43 +0100 (BST) To: bionet-software-srs@net.bio.net From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Data directories for Grid computing: SRS-LDAP test Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200207091553.g69FrWK14435@cricket.bio.indiana.edu> X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 248F117AAD for ; Tue, 9 Jul 2002 16:50:39 +0100 (BST) X-Received: from cricket.bio.indiana.edu (cricket.bio.indiana.edu [129.79.225.189]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8072017B31 for ; Tue, 9 Jul 2002 16:50:33 +0100 (BST) X-Received: (from gilbertd@localhost) by cricket.bio.indiana.edu (8.11.6+Sun/8.11.6) id g69FrWK14435 for bio-srs@net.bio.net; Tue, 9 Jul 2002 10:53:32 -0500 (EST) X-To: bio-srs@net.bio.net Date: Thu, 11 Jul 2002 11:28:21 +0100 (BST) X-Razor-id: 007340f1ba686c1371432638a3cbbf815e4eaf43 Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear folks w/ interests in bio-data distribution, I've put together an experimental SRS6-LDAP gateway tool, available at http://iubio.bio.indiana.edu/grid/directories/ This is in a very preliminary stage, essentially it is just far enough along to assess its efficiency for bulk bio-sequence search and retreival via LDAP (lightweight directory access protocol). If you are interested in trying it out, there are two simple ldapsearch programs (java and perl) here, which have test cases to the IUBio Archive SRS system. They should work on most computers. A basic LDAP url for this is ldap://iubio.bio.indiana.edu:3895/srv=srs which serves the same databanks as http://iubio.bio.indiana.edu/srs/ The source code for the SRS6-LDAP backend is included here, but I haven't gotten documentation to a usable point - anyone trying this out, let me know where I can help (besides the SRS6 binary distribution you will need openldap2 (www.openldap.org) and a C-Perl tool (for ldap to srs query conversion). In comparison to the SRS6 tools "getz" (commandline) and "wgetz" (web backend), it looks efficient and capable. E.g. it performs about the same speed over network as the local getz program, and about 3x faster than wgetz over http, without adding any binary encoded sequence formats (something you can do in LDAP, which uses binary encoded ASN.1 as its transport stream). E.g., it takes just a second or two to do a query, but to retrieve sequence the time is proportional to number of sequence records: 1.4 minutes for 20,000 records; 7 minutes for 350,000 records, 30 minutes for some 1.2 million records in GenBank which mention 'human'. -- Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu --- From owner-bio-srs@hgmp.mrc.ac.uk Thu Jul 11 11:29:00 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 7459C17B1B for ; Thu, 11 Jul 2002 11:28:57 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8568F17AD1 for ; Thu, 11 Jul 2002 11:28:50 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 1F14117A8E; Thu, 11 Jul 2002 11:28:27 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DE06417B84 for ; Wed, 10 Jul 2002 00:25:55 +0100 (BST) Received: from sjc3-1.relay.mail.uu.net (sjc3-1.relay.mail.uu.net [199.171.54.122]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5CDB017B78 for ; Wed, 10 Jul 2002 00:25:52 +0100 (BST) Received: from smtp8.google.com by sjc3sosrv11.alter.net with ESMTP (peer crosschecked as: smtp8.google.com [216.239.33.28]) id QQmwvd25769 for ; Tue, 9 Jul 2002 23:25:50 GMT Received: from sjins2.sj.google.com (proxy.google.com [216.239.35.5]) by smtp8.google.com (8.12.2/8.12.3) with ESMTP id g69NPnX5029562 for ; Tue, 9 Jul 2002 16:25:49 -0700 Received: from sjmm36.sj.google.com (sjmm36.prod.google.com [10.6.39.36]) by sjins2.sj.google.com (8.9.3/8.9.3) with ESMTP id QAA01549 for ; Tue, 9 Jul 2002 16:25:44 -0700 Received: (from news@localhost) by sjmm36.sj.google.com (8.9.3/8.9.3) id QAA29099 for bionet-software-srs@moderators.isc.org; Tue, 9 Jul 2002 16:25:47 -0700 To: bionet-software-srs@moderators.isc.org From: d_newsham@hotmail.com (D Newsham) Newsgroups: bionet.software.srs Subject: ITIS Database in Oracle script files? Organization: http://groups.google.com/ Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: posting.google.com 1026257147 29098 127.0.0.1 (9 Jul 2002 23:25:47 GMT) X-Complaints-To: groups-abuse@google.com NNTP-Posting-Date: 9 Jul 2002 23:25:47 GMT Date: Thu, 11 Jul 2002 11:28:27 +0100 (BST) X-Razor-id: 1acbe0c94975c2b6320abde11758272f78da43cf Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hi, I am not sure if this is the right newsgroup or not... so apologize in advance if it is not! I am working on a project to catalog several collections of scientific data. I plan on using the taxonomy database from ITIS (Integrated Taxonomic Information System) as the taxa reference for this database and have downloaded the full database in Informix format from their site. My question is - does anybody have the script files for converting this database to Oracle? I emailed ITIS and they said they know it has been done but could not give me any references to people who have done it. Thanks for any advice, Dina Newsham Northern Arizona University From owner-bio-srs@hgmp.mrc.ac.uk Thu Jul 18 11:31:32 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 15A7017A7B for ; Thu, 18 Jul 2002 11:31:31 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5DA2517B3B for ; Thu, 18 Jul 2002 11:31:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 2691917A6F; Thu, 18 Jul 2002 11:30:51 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AB01717D90 for ; Wed, 17 Jul 2002 18:02:05 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id C61FD17D91; Wed, 17 Jul 2002 18:01:57 +0100 (BST) To: bionet-software-srs@net.bio.net From: willy.valdivia@ndsu.nodak.edu ("Willy Valdivia Granda") Newsgroups: bionet.software.srs Subject: RE: Second Virtual Conference on Genomics and Bioinformatics Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 60FD817D8B for ; Wed, 17 Jul 2002 18:01:52 +0100 (BST) X-Received: from smtp1.ndsu.nodak.edu (smtp1.ndsu.NoDak.edu [134.129.111.146]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E5DF217D91 for ; Wed, 17 Jul 2002 18:01:50 +0100 (BST) X-Received: from datasurg14 (ndas026.ndsu.NoDak.edu [134.129.110.30]) by smtp1.ndsu.nodak.edu (8.12.1/8.12.1) with SMTP id g6HH1mHZ017997 for ; Wed, 17 Jul 2002 12:01:49 -0500 X-To: X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-In-reply-to: X-Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Date: Thu, 18 Jul 2002 11:30:51 +0100 (BST) X-Razor-id: a396cf979d1bc14c4cb825b601c7cb12c78872e3 Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Second Virtual Conference on Genomics and Bioinformatics Sharing Knowledge with the World (No registration fees) September 24-26, 2002 http://www.ndsu.nodak.edu/virtual-genomics/upcom2.htm Deadline: August 15, 2002 for complete documents Speakers List http://www.ndsu.nodak.edu/virtual-genomics/program.htm Review Committee List http://www.ndsu.nodak.edu/virtual-genomics/reviewpanel.htm Remote Locations: North Dakota State Universty, ND, (USA) Host Access Grid Academia Sinica, Taipei (TAIWAN) Real Player Version ACCESS DC, Arlington, VA (USA) Access Grid Version Boston University, MA (USA) Access Grid Version CINECA AG Conference Facility, Bologna. (ITALY) Access Grid Version Marshall University, WV (USA) Real Player Version Montclair State University, NJ (USA) Real Player Version Ohio Supercomputer Center, (OH) (USA) Access Grid Version Oklahoma State Universityn, OK (USA) Real Player Version Purdue University, West Lafayette, (IN) (USA) Access Grid Version The University of Manchester, Manchester (UK) Access Grid Version University of Hawaii, HI (USA) Access Grid Version University of Kansas, KS (USA) Access Grid Version University of Kentucky, KY (USA) Access Grid Version University of Maine, (ME) (USA) Access Grid Version University of Nebraska-Lincoln, (NE) (USA) Access Grid Version University of New Mexico HPCERC, (NM) (USA) Access Grid Version University of North Dakota, ND (USA) Real Player Version University of Puerto Rico, San Juan. Puerto Rico Access Grid Version Vrije Universiteit, Amsterdam, Amsterdam. The Netherlands Access Grid Version The "Virtual Conference on Genomics and Bioinformatics" is an advanced environment for the exchange and discussion of information related to innovations of the post-genomic era. Since genomic research has led to an explosive rate of data accumulation and to a shift in the way biological research is conducted, the conference features high profile researchers and educators working actively in the development of new applications in the areas of genomics and bioinformatics. While genomic technologies offer an enormous scientific potential to understand genome functions, structure and interaction, the increasing amount of data generated present new challenges for biologists, sociologists, mathematicians, computer scientists and biological modelers. Therefore the main goals of the Virtual Conference in Genomics and Bioinformatics are: 1) Transcend geographical and economical barriers to the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. 2) Address the benefits and limitations of the newest developments in post-genomic technologies. 3) Explore the social and ethical implications of genomic and bioinformatic research 4) Establish new ways to introduce high school community about today's multidisciplinary science. Topics of the Virtual Conference includes but not limited to: . Structural and Functional Genomics . Post-Genomic Data Standardization, Management, and Integration . Statistical and Computational Approaches for Gene Expression Analysis . Sequence Annotation . Metabolic Profiling and Simulation of Cellular Processes . Social and Ethical Implications of Genomic Research . High Throughput Computing and Distributed Memory Infrastructures Willy Valdivia Granda Plant Stress Genomics and Bioinformatics Group North Dakota State University PO BOX 5130 Fargo, USA 701 231-8440 (Lab) 701 231 8255 (Fax) www.ndsu.edu/virtual-genomics ---