From owner-embldatabank@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!EU.net!Germany.EU.net!news.dfn.de!urmel.informatik.rwth-aachen.de!news.rhrz.uni-bonn.de!ibm.rhrz.uni-bonn.de!UZS13B From: UZS13B@ibm.rhrz.uni-bonn.de (Stefan Kahlert) Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank Subject: How to search just on promoter-sequences? Date: Wed, 02 Nov 94 14:59:12 MEZ Organization: RHRZ Uni-Bonn Lines: 15 Message-ID: <17062D2C0S85.UZS13B@ibm.rhrz.uni-bonn.de> NNTP-Posting-Host: ibm.rhrz.uni-bonn.de Xref: biosci bionet.molbio.embldatabank:383 bionet.molbio.genbank:1815 Dear Colleagues I am looking for a certain sequence (a binding-motif) only in *promoters*. Fasta allows to search whole genes but only promoters are interesting for my problem. I don't have an idea how to do a search only on promoters. It would be very helpful if you could just tell me how to get a helpfile from the server that does searching on a promoter-database. Thanks a lot for your help... Stefan Kahlert Medical Polyclinic University of Bonn From owner-embldatabank@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!rutgers!gatech!udel!news.sprintlink.net!EU.net!uunet!heifetz.msen.com!emory!usenet From: bcresas@bimcore.emory.edu (Scott Sammons) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: E. coli Database Collection --> GCG format Date: 2 Nov 1994 20:28:59 GMT Organization: Biomolecular Computing Resource, Emory University Lines: 16 Distribution: world Message-ID: <398sqb$79b@emory.mathcs.emory.edu> Reply-To: bcresas@bimcore.emory.edu NNTP-Posting-Host: bimcore.cc.emory.edu Xref: biosci bionet.software.gcg:801 bionet.software:9889 bionet.molbio.embldatabank:384 Greetings: Has anyone successfully reformatted the ECD data into GCG formatted databases. The program embltogcg core dumps when I try it with one of the ECD .dat files. Scott Sammons ======================================================================= | Scott A. Sammons (404) 727-2780 | | Emory University FAX: (404) 727-3659 | | Biomolecular Computing Resource | | 3025 Rollins Research Center Email: sammons@bimcore.emory.edu | | Atlanta, GA 30322 | ======================================================================= From owner-embldatabank@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@staffa.sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: Re: E. coli Database Collection --> GCG format Date: 03 Nov 1994 09:45:14 GMT Organization: University of Cambridge, England Lines: 24 Distribution: world Message-ID: References: <398sqb$79b@emory.mathcs.emory.edu> NNTP-Posting-Host: staffa.sanger.ac.uk In-reply-to: bcresas@bimcore.emory.edu's message of 2 Nov 1994 20:28:59 GMT Xref: biosci bionet.software.gcg:802 bionet.software:9901 bionet.molbio.embldatabank:385 In article <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: > Has anyone successfully reformatted the ECD data into GCG formatted databases. > The program embltogcg core dumps when I try it with one of the ECD .dat > files. As I am involved in both ECD and EGCG, I will try to put something into EGCG 8.0 when it is ready. I take it you are referring to the very latest (new format) ECD here. Do you mean the genorf.dat file or the contigs/*.dna files (which are closer to EMBL format and have more sequence data)? Beware though - E.coli sequencing is now going so well that ECD has a contig (and more to follow) over the 350k mark, which will give some problems with GCG. Another option would be to use a script (or Perl) to reformat into enough of an "EMBL" format for EMBLtoGCG to accept it. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-embldatabank@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!cea.fr!usenet From: cisitm@albert.cad.cea.fr (Pierre Didierjean) Newsgroups: bionet.molbio.embldatabank Subject: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: 3 Nov 1994 16:17:03 GMT Organization: SSII Lines: 28 Sender: cisitm@albert.cad.cea.fr Message-ID: <39b2dv$9pd@anemone.saclay.cea.fr> NNTP-Posting-Host: nyassa.cad.cea.fr I'd like to know what kind of people i find on the net. Students, Commercials, Adminitrations, Scientifics or what ?? Is anybody knows that or have statistical results ? What are YOU doing in life ? I am a system administrator. Thanks for the answers and sorry for my english ..... Bye +-----------------------------------------------------------------------------+ | Pierre DIDIERJEAN | | | | Administrateur Systeme UNIX | | Cisi, Aix-en-Provence | | France | +-----------------------------------------------------------------------------+ | email : cisitm@albert.cad.cea.fr | +-----------------------------------------------------------------------------+ From owner-embldatabank@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!agate!darkstar.UCSC.EDU!pellinore!rafael From: rafael@cse.ucsc.edu (David Konerding) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: Re: E. coli Database Collection --> GCG format Followup-To: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Date: 3 Nov 1994 21:14:47 GMT Organization: UC Santa Cruz CIS/CE Lines: 38 Distribution: world Message-ID: <39bjs7$t3p@darkstar.UCSC.EDU> References: <398sqb$79b@emory.mathcs.emory.edu> NNTP-Posting-Host: pellinore.cse.ucsc.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software.gcg:805 bionet.software:9916 bionet.molbio.embldatabank:387 Peter Rice (pmr@staffa.sanger.ac.uk) wrote: : In article <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: : > Has anyone successfully reformatted the ECD data into GCG formatted databases. : > The program embltogcg core dumps when I try it with one of the ECD .dat : > files. : As I am involved in both ECD and EGCG, I will try to put something into EGCG 8.0 : when it is ready. I take it you are referring to the very latest (new format) : ECD here. Do you mean the genorf.dat file or the contigs/*.dna files (which are : closer to EMBL format and have more sequence data)? : Beware though - E.coli sequencing is now going so well that ECD has a contig (and : more to follow) over the 350k mark, which will give some problems with GCG. : Another option would be to use a script (or Perl) to reformat into enough of an : "EMBL" format for EMBLtoGCG to accept it. Hmm. Can anybody give me a pointer to where I can find the ECD? I am writing a thesis which regards computational methods for finding genes in prokaryotic DNA, and any database more complete than EcoSeq6 would be great. Thanks. : -- : ------------------------------------------------------------------------ : Peter Rice | Informatics Division : E-mail: pmr@sanger.ac.uk | The Sanger Centre : Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, : Fax: (44) 1223 494919 | Cambs, CB10 1RQ : URL: http://www.sanger.ac.uk/~pmr | England -- -- O~_ ------------- David Konerding (University of California, Santa Cruz) c/ /' ------- rafael@cse.ucsc.edu ( ) \( ) --- rafael@cats.ucsc.edu From owner-embldatabank@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@staffa.sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: Re: E. coli Database Collection --> GCG format Followup-To: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Date: 03 Nov 1994 22:44:38 GMT Organization: University of Cambridge, England Lines: 29 Distribution: world Message-ID: References: <398sqb$79b@emory.mathcs.emory.edu> <39bjs7$t3p@darkstar.UCSC.EDU> NNTP-Posting-Host: staffa.sanger.ac.uk In-reply-to: rafael@cse.ucsc.edu's message of 3 Nov 1994 21:14:47 GMT Xref: biosci bionet.software.gcg:806 bionet.software:9918 bionet.molbio.embldatabank:388 In article <39bjs7$t3p@darkstar.UCSC.EDU> rafael@cse.ucsc.edu (David Konerding) writes: > Peter Rice (pmr@staffa.sanger.ac.uk) wrote: > : In article <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: > : > Has anyone successfully reformatted the ECD data into GCG formatted databases. > : > The program embltogcg core dumps when I try it with one of the ECD .dat > : > files. > > : As I am involved in both ECD and EGCG, I will try to put something into EGCG 8.0 > : when it is ready. I take it you are referring to the very latest (new format) > : ECD here. Do you mean the genorf.dat file or the contigs/*.dna files (which are > : closer to EMBL format and have more sequence data)? > > Hmm. Can anybody give me a pointer to where I can find the ECD? I am writing > a thesis which regards computational methods for finding genes in prokaryotic > DNA, and any database more complete than EcoSeq6 would be great. The latest ECD is available from ftp.ebi.ac.uk in directory pub/databases/ecdc (note the extra c at the end :-) The new format is described in: Kroeger et al. (1994); Nucleic Acids Research 22:3450-3455. The contigs directory has the non-redundant contiguous sequences from E.coli K-12. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-embldatabank@net.bio.net Wed Nov 02 22:00:00 1994 Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!EU.net!sun4nl!sci.kun.nl!jackl From: jackl@sci.kun.nl (Jack Leunissen) Subject: Re: E. coli Database Collection --> GCG format Message-ID: Sender: news@sci.kun.nl (News owner) Nntp-Posting-Host: wn2.sci.kun.nl Organization: University of Nijmegen, The Netherlands References: <398sqb$79b@emory.mathcs.emory.edu> Date: Thu, 3 Nov 1994 21:57:55 GMT Lines: 17 Xref: biosci bionet.software.gcg:807 bionet.software:9921 bionet.molbio.embldatabank:389 In <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: >Has anyone successfully reformatted the ECD data into GCG formatted databases. >The program embltogcg core dumps when I try it with one of the ECD .dat >files. You might try my program "embl2nbrf", which reformats EMBL-formatted data into NBRF (=PIR) format. GCG handles this, provided you change the format identifier in the .header file from GCG into NBRF. You can find the program at "ftp.caos.kun.nl", via anonymous FTP, in the directory "pub/molbio/embl2nbrf". Best regards, Jack Leunissen CAOS/CAMM Center From owner-embldatabank@net.bio.net Sun Nov 06 22:00:00 1994 Newsgroups: bionet.molbio.embldatabank Path: biosci!rutgers!gatech!swrinde!pipex!uunet!utcsri!utnut!nott!cunews!freenet.carleton.ca!FreeNet.Carleton.CA!af910 From: af910@FreeNet.Carleton.CA (Tom Trottier) Subject: Is there anyone there? Message-ID: Sender: news@freenet.carleton.ca (Usenet News Admin) Reply-To: af910@FreeNet.Carleton.CA (Tom Trottier) Organization: The National Capital FreeNet Date: Mon, 7 Nov 1994 19:29:26 GMT Lines: 7 Tom -- \ \~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\ \Tom Trottier 613 594-4829 fax:594-8944 af910@freenet.carleton.ca\ \Information Animation, 199 Holmwood Ave Ottawa ON Canada K1S 2P3 \ \___________________________________________________________________\ From owner-embldatabank@net.bio.net Wed Nov 09 22:00:00 1994 Newsgroups: bionet.molbio.embldatabank Path: biosci!agate!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Re: Is there anyone there? Message-ID: Sender: news@ebi.ac.uk (Mr news) Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] References: Date: Thu, 10 Nov 1994 09:42:36 GMT Lines: 30 Tom Trottier (af910@FreeNet.Carleton.CA) wrote: :Is there anyone there? : Tom : -- : \ \~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\ : \Tom Trottier 613 594-4829 fax:594-8944 af910@freenet.carleton.ca\ : \Information Animation, 199 Holmwood Ave Ottawa ON Canada K1S 2P3 \ : \___________________________________________________________________\ where is there? I know I'm here. Jeroen -- ====================================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@ebi.ac.uk O O O O( *o )O O ++44 1223 494422 )O O O O o* O O( O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O O O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ====================================================================== From owner-embldatabank@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!pipex!uunet!newsfeed.ACO.net!info.univie.ac.at!coil!gl From: gl@coil.mdy.univie.ac.at (Gerald Loeffler) Newsgroups: bionet.molbio.embldatabank Subject: Re: Is there anyone there? Date: 10 Nov 1994 12:49:40 GMT Organization: Inst. for Theoretical Chemistry / Univ. of Vienna Lines: 16 Sender: gl@coil (Gerald Loeffler) Distribution: world Message-ID: <39t4t4$6e6@infosrv.edvz.univie.ac.at> References: NNTP-Posting-Host: coil.mdy.univie.ac.at yes -- Gerald Loeffler PhD student in Theoretical Biochemistry Email: gl@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 Mail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria Chauvinistic Statement: "Austria Erit In Orbe Ultima" From owner-embldatabank@net.bio.net Fri Nov 11 22:00:00 1994 Newsgroups: bionet.molbio.yeast,bionet.molbio.embldatabank Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: How much yeast is known? [Re: Progress Report YEAST Genome Sequencing] Message-ID: <1994Nov12.071107.19651@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <39dl63$kiu@rc1.vub.ac.be> Date: Sat, 12 Nov 1994 07:11:07 GMT Lines: 47 Xref: biosci bionet.molbio.yeast:1888 bionet.molbio.embldatabank:393 Colleagues, I got an inquiry of a colleague (not woking at the Biozentrum, but within our EMBnet services) on what fraction of the yeast genome is sequenced, resp. available if a BLAST, FASTA or MPsrch request is launched. I screened the archive and found the data recently posted to the yeast bb. Just for the sake of a correct answer on the second question, I would like to ask the following questions related to the included posting. Mordant Philippe (pmordant@rc1.vub.ac.be) wrote: : ********************************************************************* : * * : * IN EMBL + GENBANK + MIPS + SDB ON NOVEMBER 01, 1994 * : * PROGRESS REPORT FOR THE SYSTEMATIC SEQUENCING OF THE YEAST GENOME * : * * : ********************************************************************* Does this include MIPS sequences which are kept confidential, i.e. not being available to the non-MIPS-customer research community? [...] : --------------------------------------------------------------------- : submitted estimated new in : up today length october 94 : (kb) (kb) (%) (kb) : --------------------------------------------------------------------- [...] : ---------------------------------------------------------------- : TOTAL YEAST GENOME 5687 12400 46% 669 : ---------------------------------------------------------------- [...] As there is a considerable amount of yeast sequences already published in the sequence database (with functions etc. assigned), what would be a more customer-oriented guess on what fraction of sequences is available to the community in the EMBL database? Regards Reinhard -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-embldatabank@net.bio.net Fri Nov 11 22:00:00 1994 Path: biosci!agate!news.Stanford.EDU!fafner.Stanford.EDU!cherry From: cherry@fafner.Stanford.EDU (Mike Cherry) Newsgroups: bionet.molbio.yeast,bionet.molbio.embldatabank Subject: Re: How much yeast is known? [Re: Progress Report YEAST Genome Sequencing] Date: 12 Nov 1994 17:34:20 GMT Organization: Stanford University Genetics Department Lines: 48 Message-ID: <3a2uas$42r@nntp.Stanford.EDU> References: <39dl63$kiu@rc1.vub.ac.be> <1994Nov12.071107.19651@comp.bioz.unibas.ch> NNTP-Posting-Host: fafner.stanford.edu Xref: biosci bionet.molbio.yeast:1889 bionet.molbio.embldatabank:394 In article <1994Nov12.071107.19651@comp.bioz.unibas.ch>, Reinhard Doelz wrote: >Mordant Philippe (pmordant@rc1.vub.ac.be) wrote: > >: * IN EMBL + GENBANK + MIPS + SDB ON NOVEMBER 01, 1994 * >: * PROGRESS REPORT FOR THE SYSTEMATIC SEQUENCING OF THE YEAST GENOME * > >Does this include MIPS sequences which are kept confidential, i.e. >not being available to the non-MIPS-customer research community? I believe the answer is yes. The numbers posted by Dr. Philippe appear to include non-public sequences held at MIPS or at one of the other sequencing centers around the world. These would be regions that are considered almost done and now being annotated and verified, but not yet submitted to the public databases. Note that SGD, which might be what is referred to as SDB above, only contains publicly available sequences. That is, SGD does not contain any sequences that are not already in GenBank/EMBL. >: submitted estimated new in >: up today length october 94 >: (kb) (kb) (%) (kb) >: TOTAL YEAST GENOME 5687 12400 46% 669 > >As there is a considerable amount of yeast sequences already published >in the sequence database (with functions etc. assigned), what would be >a more customer-oriented guess on what fraction of sequences is available >to the community in the EMBL database? We estimate that 52% of the S. cerevisiae genome is present in GenBank/EMBL. This estimate includes some analysis that we have done on yeast sequences in GenBank. We built a non-redundant set of sequences, or a consensus sequence contig, out of the GenBank sequences. When the consensus sequences are combined with the genomic sequencing results we obtain a number of 6.4Mbp. The amount of publicly available sequences expected from the genomic sequencing projects should increase by 4Mbp in 1995. Thus it is advised that you regularly search the GenBank/EMBL on the chance that your region of interest has been made public. Mike J. Michael Cherry Internet: cherry@genome.stanford.edu Head, Computing Stanford DNA Sequence & Tech. Center Project Manager Saccharomyces Genome Database Stanford University School of Medicine Stanford, CA 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 From owner-embldatabank@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunic!news.funet.fi!hydra.Helsinki.FI!news.helsinki.fi!kruuna!zheng From: zheng@cc.Helsinki.FI (Huanquan Zheng) Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank Subject: pET22b sequence needed Date: 14 Nov 1994 13:47:51 GMT Organization: University of Helsinki Lines: 8 Message-ID: <3a7pq7$jpe@oravannahka.Helsinki.FI> NNTP-Posting-Host: kruuna.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL0] Xref: biosci bionet.molbio.embldatabank:395 bionet.molbio.genbank:1822 I can not find the pET22b in both databases EMBL and GenBank, any hint? Thanks! -- Huanquan Zheng ~{V#;7H*#,KD4(HK#,;lHUWS5D#,~} From owner-embldatabank@net.bio.net Sun Nov 13 22:00:00 1994 Newsgroups: bionet.molbio.yeast,bionet.molbio.embldatabank Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!tflores From: tflores@ebi.ac.uk (Tom Flores) Subject: Re: How much yeast is known? [Re: Progress Report YEAST Genome Sequencing] Message-ID: Lines: 43 Sender: news@ebi.ac.uk (Mr news) Reply-To: tflores@ebi.ac.uk (Tom Flores) Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-16 References: <39dl63$kiu@rc1.vub.ac.be> <1994Nov12.071107.19651@comp.bioz.unibas.ch> Date: Mon, 14 Nov 1994 11:34:44 GMT Xref: biosci bionet.molbio.yeast:1895 bionet.molbio.embldatabank:396 In article <1994Nov12.071107.19651@comp.bioz.unibas.ch>, Reinhard Doelz writes: > >As there is a considerable amount of yeast sequences already published >in the sequence database (with functions etc. assigned), what would be >a more customer-oriented guess on what fraction of sequences is available >to the community in the EMBL database? > and In article <3a2uas$42r@nntp.Stanford.EDU>, Mike Cherry writes: > >We estimate that 52% of the S. cerevisiae genome is present in >GenBank/EMBL. This estimate includes some analysis that we have done >on yeast sequences in GenBank. We built a non-redundant set of >sequences, or a consensus sequence contig, out of the GenBank >sequences. When the consensus sequences are combined with the genomic >sequencing results we obtain a number of 6.4Mbp. The amount of >publicly available sequences expected from the genomic sequencing >projects should increase by 4Mbp in 1995. Thus it is advised that you >regularly search the GenBank/EMBL on the chance that your region of >interest has been made public. > I recently carried out a survey for the EC in which the amount of database redundancy was estimated. In release 39 of EMBL it was estimated that there was 34.8% redundancy for Saccharomyces cerevisiae in FUN.DAT. If we apply this value to release 40 (12th September 1994) of the EMBL database with 9.8Mb of sequence we also get a figure of 6.4Mb in agreement of the above figure. Tom -- ================================================ Tomas Flores PhD Tel:+44-(0)1223 494414 The EBI Data Library Fax:+44-(0)1223 494400 Hinxton Hall Email:flores@ebi.ac.uk Hinxton Cambridge CB10 1RQ UK "FLAMES >> /dev/null" ================================================ From owner-embldatabank@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!sgiblab!spool.mu.edu!howland.reston.ans.net!usc!nic-nac.CSU.net!newshub.sdsu.edu!lif_sci_n3-mac8.sdsu.edu!user From: vnewman@lifsci.sdsu.edu (Vicky Newman) Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank Subject: Re: pET22b sequence needed Date: 15 Nov 1994 23:25:07 GMT Organization: SDSU Biology Lines: 17 Message-ID: References: <3a7pq7$jpe@oravannahka.Helsinki.FI> NNTP-Posting-Host: lif_sci_n3-mac8.sdsu.edu Xref: biosci bionet.molbio.embldatabank:397 bionet.molbio.genbank:1824 In article <3a7pq7$jpe@oravannahka.Helsinki.FI>, zheng@cc.Helsinki.FI (Huanquan Zheng) wrote: > I can not find the pET22b in both databases EMBL and GenBank, > any hint? > > Thanks! > > Zheng, Novagen is the company that makes that plasmid and they sell a computer disk with the sequences in them. The disk cost $15. I do not know of any other way to get the sequences unless you know someone who already has it. Vicky From owner-embldatabank@net.bio.net Wed Nov 16 22:00:00 1994 Newsgroups: bionet.molbio.embldatabank Path: biosci!ns1.faseb.org!darwin.sura.net!howland.reston.ans.net!pipex!uunet!newsgate.watson.ibm.com!hawnews.watson.ibm.com!puffin!dflash From: dflash@watson.ibm.com (The dFLASH Project) Subject: dFLASH server for latest GenBank/PIR/SwissProt (Release 1.1.0) Sender: news@hawnews.watson.ibm.com (NNTP News Poster) Message-ID: Date: Thu, 17 Nov 1994 17:20:48 GMT Disclaimer: This posting represents the poster's views, not necessarily those of IBM. Nntp-Posting-Host: puffin.watson.ibm.com Organization: IBM T.J. Watson Research Lines: 476 The dFLASH Group wishes to announce release 1.1.0 of the dFLASH electronic mail server. Beginning with this release of the server, we will be supporting the latest release of the GENBANK, PIR and SWISSPROT databases. In particular, users can now carry out searches in GENBANK Release 85 (September 30, 1994) PIR Release 42 (September 30, 1994) --> DEFAULT Database <-- SWISSPROT Release 30 (October 30, 1994) Full bibliographic references can optionally be included with the computed alignments, for all three databases. Notice that a number of necessary changes and additions have been incorporated in the "query language". For example, since we now support a larget set of databases, "target protein" is not a valid directive anymore! The appended help file describes the changes and available functions in detail. NEW FEATURES: o the reported results can now be sorted using a sorting key specified by the user via the "query language" o a smart-email filter has been implemented: various specification errors are now caught and corrected automatically; notifications are sent to the user for all taken actions. It is our intention to update the server with the latest release of each of the above dbases within the first two weeks after it becomes available. The server is accessible through the Internet and is now operating 24 hours a day, 7 days a week and can be accessed both directly and through "Grail" of the Oak Ridge National Lab. Sincerely, The dFLASH Group ------------------------------> CUT HERE <----------------------------------- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! The dFLASH server now supports the GenBank, PIR and SWISSPROT databases. !! !! The supported releases are: !! !! GENBANK Release 85 (September 30, 1994) !! !! PIR Release 42 (September 30, 1994) --> DEFAULT Database <-- !! !! SWISSPROT Release 30 (October 30, 1994) !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! N O T A B E N E !! !! The dFLASH server is still under development. If some of the answers do !! !! not make sense it is very likely that this is due to a bug in our code. !! !! Please, email bug reports and comments to dflash@watson.ibm.com with !! !! subject line "bug" or "comments". !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Dear User, welcome to Release 1.1.0 of the the dFLASH server! The dFLASH server is a "homologous sequence retrieval" program for PROTEIN and DNA sequences. dFLASH is a parallel system running on an IBM SP/x architecture. Intra-node communication, evidence integration and alignment are performed in parallel. The system has been implemented using IBM's Concert/C language for distributed programming. The server is available 24 hours a day, 7 days a week and can be accessed both directly and through "Grail" of the Oak Ridge National Lab. Incremental changes and improvements made to the server will be reflected in the "Message of the day" at the beginning of this help file: we recommend that users periodically issue a `send help' request for up to date information on the server. For the moment, we can process requests originating from email addresses of the form user@[machine.][subdomain.]institution.type or user%machine@[machine.][subdomain.]institution.type or "string::user"@[machine.][subdomain.]institution.type We plan to further expand the accepted formats, depending on demand. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ HOW TO USE THE SERVER: You can use the dFLASH facilities by sending an email ---------------------- message with the appropriate syntax to the address "dflash@watson.ibm.com" (without the quotes). SUBJECT LINE: It is important that the "Subject" line of your message contain ------------- one of: { dflash, dFlash, dFLASH, DFLASH }. Messages whose subject line does NOT conform to this rule, **WILL BE LEFT UNPROCESSED**. The reason for that restriction is that we want to be able to automatically distinguish between messages that are addressed to the server and those that are meant for one of the group members. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ MESSAGE FORMAT: The typical message-body of an email request looks as follows --------------- BLOSUM 62 (optional | DIRECTIVE) VERBOSE 10 20 (optional | DIRECTIVE) SEQUENCES 100 (optional | DIRECTIVE) ALIGNMENTS 50 (optional | DIRECTIVE) THRESHOLD 30 (optional | DIRECTIVE) KEY XMATCH (optional | DIRECTIVE) SOURCE PROTEIN (optional | DIRECTIVE) TARGET SP (optional | DIRECTIVE) BEGIN (mandatory | DIRECTIVE) >A_ONE_LINE_TEST_SEQ_LABEL (mandatory -- notice the '>' ) a_sequence_of_{amino_acids,nucleic_acids,spaces,tabs} 1 (mandatory terminator) The PAM/BLOSUM, VERBOSE, SEQUENCES, ALIGNMENTS, THRESHOLD, KEY, SOURCE and TARGET directives can appear in any order but they *must* precede the BEGIN directive. The BEGIN line must be followed by the LABEL line which in turn should be followed by the test sequence. The test sequence should contain at least 18(=proteins)/54(=dna) and not more than 1500 amino acid or nucleotide characters. But it may contain ANY NUMBER of CARRIAGE RETURN TAB and SPACE characters; the latter are not of course counted while computing the length of the test sequence. There is NO case sensitivity in the label and the test sequence itself. If the test sequence is longer than 1500 characters, the e-mail filter will truncate it to the first 1500 characters and will send a note to that effect to the originator of the query; the filter will then submit the truncated sequence to the search engine. NOTA BENE: The words appearing on the lines marked DIRECTIVE above can be in ---------- lower case or upper case; in other words, you can have pam or PAM, threshold or THRESHOLD, alignments or ALIGNMENTS, etc. However, something like ThReShOlD will not work. The directive pertaining to the scoring matrix allows the user to specify the matrix to be used for computing the alignment scores. You can use either the word PAM followed by a space and the desired distance, or the word BLOSUM followed by space and the desired distance. Examples: PAM 250, BLOSUM 62 etc. If no matrix directive is included in the message, PAM 250 is used as the default. Depending on the values of the directive TARGET (see below) the matrix directive if present may be ignored. The VERBOSE line allows the sender to also retrieve the data about authors, dates, entries, superfamilies etc. that are contained in the original PIR, SwissProt and GenBank databases. This directive accepts one OR two arguments; for example: verbose 15 25 means "send me the text data for the sequences occupying positions 15 through 25 in the final ranking." On the other hand, verbose 15 means "send me the text data for the sequences occupying the first 15 positions in the final ranking." If no verbose line appears, no citation data is sent. The SEQUENCES line allows one to restrict the reported sequences to the given number. This directive controls the number of entries in the ``short list'' of recovered database sequences only. If no SEQUENCES line is given, the server code will set it to an appropriate default value (100). The ALIGNMENTS line allows one to restrict the reported alignments to the given number. If no ALIGNMENTS line is given, the server code will set it to an appropriate default value (100). The ALIGNMENTS value cannot exceed 5000. Values larger than 5000 are reduced to 5000. The THRESHOLD line allows one to restrict the number of reported sequences (and thus alignments) to only those whose Score exceeds the given THRESHOLD value. If no THRESHOLD line is given the server code will set it to an appropriate default value. The default values are 50 for DNA sequences, and 80 for protein sequences. There is also a *hard* threshold value of 40 for DNA, and 30 for PROTEIN sequences; if the user-requested values are smaller than these hard-thresholds, the requested threshold will be increased accordingly. NOTA BENE: (1) if the THRESHOLD value is too small, you are running the danger ---------- of upsetting your mailer program since chances are that you will receive a very big file as a reply from the server. (2) if the THRESHOLD is too high the list of recovered entries will be empty, or very short; you should decrease the threshold's value and resubmit your query. The KEY line allows the user to specify the key to be used when sorting the results (retrieved sequences) corresponding to a submitted search request. The keyword KEY can be followed by one of { SCORE,score, LENGTH,length, PEAK, peak, GAP,gap, MATCH,match, XMATCH,xmatch }. By setting KEY to one of {SCORE,score} the user indicates that the retrieved sequences should be sorted in decreasing order of total computed score. By setting KEY to one of {LENGTH, length} the user indicates that the retrieved sequences be sorted in decreasing order of their length. Setting KEY to one of {PEAK,peak} will result in the retrieved sequences being sorted in decreasing order of the maximum score value over *any* 18(=proteins)s or 54(=dna) residue window of the recovered match. Setting KEY to one of {GAP,gap} will result in the retrieved sequences being sorted in decreasing order of the maximum gap inserted that will result in a best alignment with the query strand. Setting KEY to one of {MATCH,match} will result in the retrieved sequences being sorted in decreasing order of the total (=conservative+exact) number of matches with the query strand. Finally, setting KEY to one of {XMATCH,xmatch} will sort the retrieved sequences in decreasing order of the number of exact matches with the query strand. If no KEY directive is specified, the retrieved sequences will be sorted in order of decreasing "score". The SOURCE line allows the user to specify the type of the query strand as being a { PROTEIN,protein, DNA,dna } sequence. By setting SOURCE to one of {PROTEIN,protein} the user indicates that the query strand is a sequence of amino acids. By setting SOURCE to one of {DNA,dna} the user indicates that the query strand is a sequence of nucleotides. The TARGET line allows the user to specify the type of the target database to be one of { PIR,pir, SP,sp, GB,gb }. This way the user controls the database in which the search will be carried out. If TARGET is set to one of {PIR,pir}, the search will take place in the PIR database. If TARGET is set to one of {SP,sp} the search will take place in the SWISSPROT database. If TARGET is set to one of {GB,gb}, the search will take place in the GenBank database. Requests for searches in unsupported databases will be *IGNORED* by the server and generate a complaint message that will be sent back to the originator of the request. If *only* SOURCE is specified, then the TARGET will be set automatically: in particular, if SOURCE is set to one of { protein, PROTEIN } then the search will be carried in the "PIR" database, whereas if source is set to one of { dna, DNA } then the search will take place in the "GB" database. If *neither* SOURCE *nor* TARGET lines are given, the server will assume it is dealing with an amino acid strand and carry out the search against the "PIR" database. The LABEL line allows the user to enter mnemonic information pertaining the the test sequence, the time of the day etc. The information of this line will be reproduced in the Subject line of the reply message. Notice that the LABEL line *must* begin with the character '>'. All the submitted messages must be terminated by the number '1' This number can follow the last character of the test sequence or be in a line by itself. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ A 'SMART' FILTER: The email filter that allows for the above message format ----------------- has been improved in this release. In particular, the filter is 'smart' enough to catch inconsistencies in the user's message. The filter will correct them and send a note to the originator of the message. *Unlike* older releases of the filter, this version will submit the corrected message to the search engine. The filter will also send one email note to the originator of the query for *every* change it has carried out; the note(s) will contain information about the actions that the filter has taken. For example, if the user's note contains the following lines sequences 20 alignments 50 verbose 10 30 the filter will reset the value of 'alignments' to 20, and of the 'verbose_to to 20, and subsequently submit the corrected query to the search engine. Since two changes took place, the filter will also send two email notes to the originator of the query detailing the actions it has taken. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ EXAMPLES: Two example inputs follow --------- Example 1: pam 250 sequences 50 alignments 30 threshold 100 target pir begin > HBA_HUMAN STANDARD; PRT; 141 AA. P01922; HEMOGLOBIN ALPHA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr will be used in the search. Not more than the 50 top scoring sequences will be reported in the short list. Also, the alignments for the top 30 scoring sequences will be returned. No reported sequence will have score that is less than 100, and the reported sequences will be sorted in order of decreasing score. The test sequence is declared to be a sequence of amino acids and should be searched against the PIR database. Example 2: BLOSUM 62 KEY XMATCH BEGIN > Sequence sent to dflash on Fri May 20 13:40:17 EDT 1994 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr" will be used in the search. The server code will set the various parameters to appropriate default values. The server will treat the test sequence as a sequence of amino acids (default) and will search against the "PIR" database (default) with a score threshold set at 80 (default). The retrieved sequences will be reported in order of decreasing number of exact matches with the query strand. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ SCORING MATRICES: ----------------- You can use both PAM and BLOSUM scoring matrices for protein searches. These can be requested via the optional { pam, PAM, blosum, BLOSUM } directive. The currently supported distances are for BLOSUM: 30, 35, 40, 45, 50, 55, 60, 62, 65, 70, 75, 80, 85, 90, 100 for PAM: 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, and 500. For DNA searches, the PAM/BLOSUM declarations are ignored $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ NOTE ON ALIGNMENT: ------------------ The server's alignment code implements the Smith-Waterman algorithm (dynamic programming) to align each of the retrieved sequences with the test input. This is *NOT* to be confused with the indexing method that we use to determine the candidates to be aligned. The meaning of the variables in the listing that is returned by the dFLASH server ..... .... Score Matrix: PAM250 Max Reported Sequences: 1000 Max Reported Alignments: 10 Score Threshold At: 65 Id Label: Score NRes Ex% Tot% Sig Pk ---------------------------------------------------------------------------- 1. HAHU hemoglobin alpha chain - human 655 141 100% 100% 100 89 2. HACZ hemoglobin alpha chain - chimpanzee 655 141 100% 100% 100 89 3. HACZP hemoglobin alpha chain - pygmy chi 655 141 100% 100% 100 89 4. HAGO hemoglobin alpha chain - lowland go 654 141 99% 100% 99 89 5. HAMQP hemoglobin alpha chain - hanuman l 653 141 97% 100% 99 89 6. B27792 hemoglobin alpha-1 chain - orangu 649 141 97% 100% 99 89 7. A25126 hemoglobin alpha-1 chain - Sumatr 649 141 97% 100% 99 89 ... ..... .. is the following: NRes: the number of residues (amino acids) in the recovered match Score: sequence similarity score of the recovered sequence based on the selected mutation matrix Ex%: percentage of *exact* matching residues Tot%: percentage of *total* (=exact+conservative) matching residues Sig: 100 times the ratio between the actual computed score and the score obtained by matching the retrieved sub-segment with itself; the denominator is the maximum obtainable score for the sub-segment in question (all gaps removed). Peak: the maximum score value over *any* 18(=proteins)s or 54(=dna) residue window of the recovered match. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ TO OBTAIN HELP: --------------- You can obtain this message at any moment by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of { help, HELP, send help, SEND HELP }. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ TO OBTAIN ON-LINE REPRINTS OF PAPERS ------------------------------------ You can obtain reprints (in PostScript) of relevant papers by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of {flashpaper, FLASHPAPER, send flashpaper, SEND FLASHPAPER } ---> returns to the originator of the request a copy of the FLASH paper that will appear in `CABIOS' one of {dflashpaper, DFLASHPAPER, send dflashpaper, SEND DFLASHPAPER } ---> returns to the originator of the request a copy of a paper that contains a description of dFLASH that has appeared in `IEEE Computational Science and Engineering' one of {concertpaper, CONCERTPAPER, send concertpaper, SEND CONCERTPAPER } ---> returns to the originator of the request a copy of a high-level paper describing the CONCERT/C language one of {bayespaper, BAYESPAPER, send bayespaper, SEND BAYESPAPER } --> returns to the originator of the request a copy of a paper describing a computer-vision application based on similar to dFLASH indexing prin- ciples that will appear in `CVGIP-IU' Notice there can only be *one* such request per message! Also, make sure you do not issue a new paper request until after the previous request has returned to you all of the postscript files and you have removed the latter from your mailbox: the returned messages are rather big (between 1 and 4 Megabytes) and are guaranteed to overflow the disk set aside for mail messages on most systems. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ Thank you for your interest in the dFLASH server. Sincerely, The dFLASH Group $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ COMMENTS?? We will appreciate receiving your feedback, suggestions, comments, ---------- or bug reports; all of these can be sent to "dflash@watson.ibm.com" Please, make sure your "Subject" line contains the word "comments" or "bug". $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ REFERENCES If you make use of the dFLASH server, please reference ---------- A. Califano and I. Rigoutsos, "FLASH: A Fast Look-up Algorithm for String Homology." In CABIOS. To appear. I. Rigoutsos and A. Califano, "Searching In Parallel for Similar Protein Strings." In IEEE Computational Science and Engineering, June 1994. If you wish to find out more, you can contact Isidore Rigoutsos and Andrea Califano at {rigoutso,acal}@watson.ibm.com $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ For more information on the Concert/C language, please refer to J. Auerbach, D. Bacon, A. Goldberg, G. Goldszmidt, A. Gopal, M. Kennedy, A. Lowry, J. Russell, W. Silverman, R. Strom, D. Yellin, and S. Yemini, "High-level language support for programming reliable distributed systems." In Proceedings of the International Conference on Computer Languages, April 1992, Oakland, California. or contact Jim Russell (jrussell@watson.ibm.com) $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ ------------------------------> CUT HERE <----------------------------------- From owner-embldatabank@net.bio.net Fri Nov 18 22:00:00 1994 Path: biosci!biosci!not-for-mail From: dflash@watson.ibm.com (The dFLASH Project) Newsgroups: bionet.announce,bionet.molbio.genbank,bionet.molbio.embldatabank Subject: dFLASH server for latest GenBank/PIR/SwissProt (Release 1.1.0) Date: 18 Nov 1994 22:25:42 -0800 Organization: IBM T.J. Watson Research Lines: 473 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Disclaimer: This posting represents the poster's views, not necessarily those of IBM. Xref: biosci bionet.announce:1583 bionet.molbio.genbank:1827 bionet.molbio.embldatabank:399 The dFLASH Group wishes to announce release 1.1.0 of the dFLASH electronic mail server. Beginning with this release of the server, we will be supporting the latest release of the GENBANK, PIR and SWISSPROT databases. In particular, users can now carry out searches in GENBANK Release 85 (September 30, 1994) PIR Release 42 (September 30, 1994) --> DEFAULT Database <-- SWISSPROT Release 30 (October 30, 1994) Full bibliographic references can optionally be included with the computed alignments, for all three databases. Notice that a number of necessary changes and additions have been incorporated in the "query language". For example, since we now support a larget set of databases, "target protein" is not a valid directive anymore! The appended help file describes the changes and available functions in detail. NEW FEATURES: o the reported results can now be sorted using a sorting key specified by the user via the "query language" o a smart-email filter has been implemented: various specification errors are now caught and corrected automatically; notifications are sent to the user for all taken actions. It is our intention to update the server with the latest release of each of the above dbases within the first two weeks after it becomes available. The server is accessible through the Internet and is now operating 24 hours a day, 7 days a week and can be accessed both directly and through "Grail" of the Oak Ridge National Lab. Sincerely, The dFLASH Group ------------------------------> CUT HERE <----------------------------------- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! The dFLASH server now supports the GenBank, PIR and SWISSPROT databases. !! !! The supported releases are: !! !! GENBANK Release 85 (September 30, 1994) !! !! PIR Release 42 (September 30, 1994) --> DEFAULT Database <-- !! !! SWISSPROT Release 30 (October 30, 1994) !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! N O T A B E N E !! !! The dFLASH server is still under development. If some of the answers do !! !! not make sense it is very likely that this is due to a bug in our code. !! !! Please, email bug reports and comments to dflash@watson.ibm.com with !! !! subject line "bug" or "comments". !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Dear User, welcome to Release 1.1.0 of the the dFLASH server! The dFLASH server is a "homologous sequence retrieval" program for PROTEIN and DNA sequences. dFLASH is a parallel system running on an IBM SP/x architecture. Intra-node communication, evidence integration and alignment are performed in parallel. The system has been implemented using IBM's Concert/C language for distributed programming. The server is available 24 hours a day, 7 days a week and can be accessed both directly and through "Grail" of the Oak Ridge National Lab. Incremental changes and improvements made to the server will be reflected in the "Message of the day" at the beginning of this help file: we recommend that users periodically issue a `send help' request for up to date information on the server. For the moment, we can process requests originating from email addresses of the form user@[machine.][subdomain.]institution.type or user%machine@[machine.][subdomain.]institution.type or "string::user"@[machine.][subdomain.]institution.type We plan to further expand the accepted formats, depending on demand. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ HOW TO USE THE SERVER: You can use the dFLASH facilities by sending an email ---------------------- message with the appropriate syntax to the address "dflash@watson.ibm.com" (without the quotes). SUBJECT LINE: It is important that the "Subject" line of your message contain ------------- one of: { dflash, dFlash, dFLASH, DFLASH }. Messages whose subject line does NOT conform to this rule, **WILL BE LEFT UNPROCESSED**. The reason for that restriction is that we want to be able to automatically distinguish between messages that are addressed to the server and those that are meant for one of the group members. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ MESSAGE FORMAT: The typical message-body of an email request looks as follows --------------- BLOSUM 62 (optional | DIRECTIVE) VERBOSE 10 20 (optional | DIRECTIVE) SEQUENCES 100 (optional | DIRECTIVE) ALIGNMENTS 50 (optional | DIRECTIVE) THRESHOLD 30 (optional | DIRECTIVE) KEY XMATCH (optional | DIRECTIVE) SOURCE PROTEIN (optional | DIRECTIVE) TARGET SP (optional | DIRECTIVE) BEGIN (mandatory | DIRECTIVE) >A_ONE_LINE_TEST_SEQ_LABEL (mandatory -- notice the '>' ) a_sequence_of_{amino_acids,nucleic_acids,spaces,tabs} 1 (mandatory terminator) The PAM/BLOSUM, VERBOSE, SEQUENCES, ALIGNMENTS, THRESHOLD, KEY, SOURCE and TARGET directives can appear in any order but they *must* precede the BEGIN directive. The BEGIN line must be followed by the LABEL line which in turn should be followed by the test sequence. The test sequence should contain at least 18(=proteins)/54(=dna) and not more than 1500 amino acid or nucleotide characters. But it may contain ANY NUMBER of CARRIAGE RETURN TAB and SPACE characters; the latter are not of course counted while computing the length of the test sequence. There is NO case sensitivity in the label and the test sequence itself. If the test sequence is longer than 1500 characters, the e-mail filter will truncate it to the first 1500 characters and will send a note to that effect to the originator of the query; the filter will then submit the truncated sequence to the search engine. NOTA BENE: The words appearing on the lines marked DIRECTIVE above can be in ---------- lower case or upper case; in other words, you can have pam or PAM, threshold or THRESHOLD, alignments or ALIGNMENTS, etc. However, something like ThReShOlD will not work. The directive pertaining to the scoring matrix allows the user to specify the matrix to be used for computing the alignment scores. You can use either the word PAM followed by a space and the desired distance, or the word BLOSUM followed by space and the desired distance. Examples: PAM 250, BLOSUM 62 etc. If no matrix directive is included in the message, PAM 250 is used as the default. Depending on the values of the directive TARGET (see below) the matrix directive if present may be ignored. The VERBOSE line allows the sender to also retrieve the data about authors, dates, entries, superfamilies etc. that are contained in the original PIR, SwissProt and GenBank databases. This directive accepts one OR two arguments; for example: verbose 15 25 means "send me the text data for the sequences occupying positions 15 through 25 in the final ranking." On the other hand, verbose 15 means "send me the text data for the sequences occupying the first 15 positions in the final ranking." If no verbose line appears, no citation data is sent. The SEQUENCES line allows one to restrict the reported sequences to the given number. This directive controls the number of entries in the ``short list'' of recovered database sequences only. If no SEQUENCES line is given, the server code will set it to an appropriate default value (100). The ALIGNMENTS line allows one to restrict the reported alignments to the given number. If no ALIGNMENTS line is given, the server code will set it to an appropriate default value (100). The ALIGNMENTS value cannot exceed 5000. Values larger than 5000 are reduced to 5000. The THRESHOLD line allows one to restrict the number of reported sequences (and thus alignments) to only those whose Score exceeds the given THRESHOLD value. If no THRESHOLD line is given the server code will set it to an appropriate default value. The default values are 50 for DNA sequences, and 80 for protein sequences. There is also a *hard* threshold value of 40 for DNA, and 30 for PROTEIN sequences; if the user-requested values are smaller than these hard-thresholds, the requested threshold will be increased accordingly. NOTA BENE: (1) if the THRESHOLD value is too small, you are running the danger ---------- of upsetting your mailer program since chances are that you will receive a very big file as a reply from the server. (2) if the THRESHOLD is too high the list of recovered entries will be empty, or very short; you should decrease the threshold's value and resubmit your query. The KEY line allows the user to specify the key to be used when sorting the results (retrieved sequences) corresponding to a submitted search request. The keyword KEY can be followed by one of { SCORE,score, LENGTH,length, PEAK, peak, GAP,gap, MATCH,match, XMATCH,xmatch }. By setting KEY to one of {SCORE,score} the user indicates that the retrieved sequences should be sorted in decreasing order of total computed score. By setting KEY to one of {LENGTH, length} the user indicates that the retrieved sequences be sorted in decreasing order of their length. Setting KEY to one of {PEAK,peak} will result in the retrieved sequences being sorted in decreasing order of the maximum score value over *any* 18(=proteins)s or 54(=dna) residue window of the recovered match. Setting KEY to one of {GAP,gap} will result in the retrieved sequences being sorted in decreasing order of the maximum gap inserted that will result in a best alignment with the query strand. Setting KEY to one of {MATCH,match} will result in the retrieved sequences being sorted in decreasing order of the total (=conservative+exact) number of matches with the query strand. Finally, setting KEY to one of {XMATCH,xmatch} will sort the retrieved sequences in decreasing order of the number of exact matches with the query strand. If no KEY directive is specified, the retrieved sequences will be sorted in order of decreasing "score". The SOURCE line allows the user to specify the type of the query strand as being a { PROTEIN,protein, DNA,dna } sequence. By setting SOURCE to one of {PROTEIN,protein} the user indicates that the query strand is a sequence of amino acids. By setting SOURCE to one of {DNA,dna} the user indicates that the query strand is a sequence of nucleotides. The TARGET line allows the user to specify the type of the target database to be one of { PIR,pir, SP,sp, GB,gb }. This way the user controls the database in which the search will be carried out. If TARGET is set to one of {PIR,pir}, the search will take place in the PIR database. If TARGET is set to one of {SP,sp} the search will take place in the SWISSPROT database. If TARGET is set to one of {GB,gb}, the search will take place in the GenBank database. Requests for searches in unsupported databases will be *IGNORED* by the server and generate a complaint message that will be sent back to the originator of the request. If *only* SOURCE is specified, then the TARGET will be set automatically: in particular, if SOURCE is set to one of { protein, PROTEIN } then the search will be carried in the "PIR" database, whereas if source is set to one of { dna, DNA } then the search will take place in the "GB" database. If *neither* SOURCE *nor* TARGET lines are given, the server will assume it is dealing with an amino acid strand and carry out the search against the "PIR" database. The LABEL line allows the user to enter mnemonic information pertaining the the test sequence, the time of the day etc. The information of this line will be reproduced in the Subject line of the reply message. Notice that the LABEL line *must* begin with the character '>'. All the submitted messages must be terminated by the number '1' This number can follow the last character of the test sequence or be in a line by itself. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ A 'SMART' FILTER: The email filter that allows for the above message format ----------------- has been improved in this release. In particular, the filter is 'smart' enough to catch inconsistencies in the user's message. The filter will correct them and send a note to the originator of the message. *Unlike* older releases of the filter, this version will submit the corrected message to the search engine. The filter will also send one email note to the originator of the query for *every* change it has carried out; the note(s) will contain information about the actions that the filter has taken. For example, if the user's note contains the following lines sequences 20 alignments 50 verbose 10 30 the filter will reset the value of 'alignments' to 20, and of the 'verbose_to to 20, and subsequently submit the corrected query to the search engine. Since two changes took place, the filter will also send two email notes to the originator of the query detailing the actions it has taken. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ EXAMPLES: Two example inputs follow --------- Example 1: pam 250 sequences 50 alignments 30 threshold 100 target pir begin > HBA_HUMAN STANDARD; PRT; 141 AA. P01922; HEMOGLOBIN ALPHA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr will be used in the search. Not more than the 50 top scoring sequences will be reported in the short list. Also, the alignments for the top 30 scoring sequences will be returned. No reported sequence will have score that is less than 100, and the reported sequences will be sorted in order of decreasing score. The test sequence is declared to be a sequence of amino acids and should be searched against the PIR database. Example 2: BLOSUM 62 KEY XMATCH BEGIN > Sequence sent to dflash on Fri May 20 13:40:17 EDT 1994 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr" will be used in the search. The server code will set the various parameters to appropriate default values. The server will treat the test sequence as a sequence of amino acids (default) and will search against the "PIR" database (default) with a score threshold set at 80 (default). The retrieved sequences will be reported in order of decreasing number of exact matches with the query strand. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ SCORING MATRICES: ----------------- You can use both PAM and BLOSUM scoring matrices for protein searches. These can be requested via the optional { pam, PAM, blosum, BLOSUM } directive. The currently supported distances are for BLOSUM: 30, 35, 40, 45, 50, 55, 60, 62, 65, 70, 75, 80, 85, 90, 100 for PAM: 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, and 500. For DNA searches, the PAM/BLOSUM declarations are ignored $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ NOTE ON ALIGNMENT: ------------------ The server's alignment code implements the Smith-Waterman algorithm (dynamic programming) to align each of the retrieved sequences with the test input. This is *NOT* to be confused with the indexing method that we use to determine the candidates to be aligned. The meaning of the variables in the listing that is returned by the dFLASH server ..... .... Score Matrix: PAM250 Max Reported Sequences: 1000 Max Reported Alignments: 10 Score Threshold At: 65 Id Label: Score NRes Ex% Tot% Sig Pk ---------------------------------------------------------------------------- 1. HAHU hemoglobin alpha chain - human 655 141 100% 100% 100 89 2. HACZ hemoglobin alpha chain - chimpanzee 655 141 100% 100% 100 89 3. HACZP hemoglobin alpha chain - pygmy chi 655 141 100% 100% 100 89 4. HAGO hemoglobin alpha chain - lowland go 654 141 99% 100% 99 89 5. HAMQP hemoglobin alpha chain - hanuman l 653 141 97% 100% 99 89 6. B27792 hemoglobin alpha-1 chain - orangu 649 141 97% 100% 99 89 7. A25126 hemoglobin alpha-1 chain - Sumatr 649 141 97% 100% 99 89 ... ..... .. is the following: NRes: the number of residues (amino acids) in the recovered match Score: sequence similarity score of the recovered sequence based on the selected mutation matrix Ex%: percentage of *exact* matching residues Tot%: percentage of *total* (=exact+conservative) matching residues Sig: 100 times the ratio between the actual computed score and the score obtained by matching the retrieved sub-segment with itself; the denominator is the maximum obtainable score for the sub-segment in question (all gaps removed). Peak: the maximum score value over *any* 18(=proteins)s or 54(=dna) residue window of the recovered match. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ TO OBTAIN HELP: --------------- You can obtain this message at any moment by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of { help, HELP, send help, SEND HELP }. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ TO OBTAIN ON-LINE REPRINTS OF PAPERS ------------------------------------ You can obtain reprints (in PostScript) of relevant papers by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of {flashpaper, FLASHPAPER, send flashpaper, SEND FLASHPAPER } ---> returns to the originator of the request a copy of the FLASH paper that will appear in `CABIOS' one of {dflashpaper, DFLASHPAPER, send dflashpaper, SEND DFLASHPAPER } ---> returns to the originator of the request a copy of a paper that contains a description of dFLASH that has appeared in `IEEE Computational Science and Engineering' one of {concertpaper, CONCERTPAPER, send concertpaper, SEND CONCERTPAPER } ---> returns to the originator of the request a copy of a high-level paper describing the CONCERT/C language one of {bayespaper, BAYESPAPER, send bayespaper, SEND BAYESPAPER } --> returns to the originator of the request a copy of a paper describing a computer-vision application based on similar to dFLASH indexing prin- ciples that will appear in `CVGIP-IU' Notice there can only be *one* such request per message! Also, make sure you do not issue a new paper request until after the previous request has returned to you all of the postscript files and you have removed the latter from your mailbox: the returned messages are rather big (between 1 and 4 Megabytes) and are guaranteed to overflow the disk set aside for mail messages on most systems. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ Thank you for your interest in the dFLASH server. Sincerely, The dFLASH Group $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ COMMENTS?? We will appreciate receiving your feedback, suggestions, comments, ---------- or bug reports; all of these can be sent to "dflash@watson.ibm.com" Please, make sure your "Subject" line contains the word "comments" or "bug". $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ REFERENCES If you make use of the dFLASH server, please reference ---------- A. Califano and I. Rigoutsos, "FLASH: A Fast Look-up Algorithm for String Homology." In CABIOS. To appear. I. Rigoutsos and A. Califano, "Searching In Parallel for Similar Protein Strings." In IEEE Computational Science and Engineering, June 1994. If you wish to find out more, you can contact Isidore Rigoutsos and Andrea Califano at {rigoutso,acal}@watson.ibm.com $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ For more information on the Concert/C language, please refer to J. Auerbach, D. Bacon, A. Goldberg, G. Goldszmidt, A. Gopal, M. Kennedy, A. Lowry, J. Russell, W. Silverman, R. Strom, D. Yellin, and S. Yemini, "High-level language support for programming reliable distributed systems." In Proceedings of the International Conference on Computer Languages, April 1992, Oakland, California. or contact Jim Russell (jrussell@watson.ibm.com) $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ ------------------------------> CUT HERE <----------------------------------- From owner-embldatabank@net.bio.net Tue Nov 22 22:00:00 1994 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!newsdist.tc.umn.edu!mayonews.mayo.edu!NewsWatcher!user From: ander@fermat.mayo.edu (RAA) Newsgroups: bionet.molbio.embldatabank Subject: Genbank Search Result????? Followup-To: bionet.molbio.embldatabank Date: 21 Nov 1994 20:05:15 GMT Organization: Mayo Foundation Lines: 6 Distribution: world Message-ID: NNTP-Posting-Host: romulus.mayo.edu I have isolated what I thought to be a new cDNA clone. I ran this against the GenBank. I found a 330 bp cDNA match that had recently been identified by a group called "Genexpress cDNA program". Does anyone know what this is? Is this a Biotech company or part of the human genome project? Any comments would be apperciated. RAA From owner-embldatabank@net.bio.net Tue Nov 22 22:00:00 1994 Newsgroups: bionet.molbio.embldatabank Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!tome From: tome@ebi.ac.uk (Patricia Rodriguez-Tome) Subject: Re: Genbank Search Result????? Message-ID: Lines: 27 Sender: news@ebi.ac.uk (Mr news) Reply-To: tome@ebi.ac.uk (Patricia Rodriguez-Tome) Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-16 References: Date: Wed, 23 Nov 1994 09:50:09 GMT In article , ander@fermat.mayo.edu (RAA) writes: >I have isolated what I thought to be a new cDNA clone. I ran this against >the GenBank. I found a 330 bp cDNA match that had recently been identified >by a group called "Genexpress cDNA program". Does anyone know what this >is? Is this a Biotech company or part of the human genome project? Any >comments would be apperciated. >RAA > The "Genexpress cDNA program" is a research project from Genethon in France Genethon is a Human Genome Research Center that has the academic status in France. If you want more information you can mail genexpress@genethon.fr or Remi.Houlgatte@isagrogn.vjf.inserm.fr Regards Pat RT -- ======================================================================= Dr. Patricia Rodriguez-Tome | Email:tome@ebi.ac.uk EBI - European Bioinformatics Institute | URL: http://www.ebi.ac.uk Hinxton Hall, Hinxton | Tel: +44 (0)223 494 414 Cambridge CB10 1RQ, UK | Fax: +44 (0)223 494 468 ======================================================================== From owner-embldatabank@net.bio.net Wed Nov 23 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.embldatabank Subject: Re: Genbank Search Result????? Date: 24 Nov 1994 10:17:55 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 22 Message-ID: <3b1p8j$2b2l@sat.ipp-garching.mpg.de> References: NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Patricia Rodriguez-Tome (tome@ebi.ac.uk) wrote: > In article , ander@fermat.mayo.edu (RAA) writes: > >I have isolated what I thought to be a new cDNA clone. I ran this against > >the GenBank. I found a 330 bp cDNA match that had recently been identified > >by a group called "Genexpress cDNA program". Does anyone know what this > >is? Is this a Biotech company or part of the human genome project? Any > >comments would be apperciated. > The "Genexpress cDNA program" is a research project from Genethon in France There is another "Genexpress cDNA program" which runs at the University of Munich. They sequence ESTs from human heart. You can contact the leader, Dr. Brigitte Obermaier, at obermaier@vms.biochem.mpg.de --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-embldatabank@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!usc!nic-nac.CSU.net!newshub.sdsu.edu!ucsnews!ucssun1!shumard From: shumard@ucssun1.sdsu.edu (shumard) Newsgroups: bionet.molbio.embldatabank Subject: what i'm doing in life Date: 28 Nov 1994 05:22:54 GMT Organization: San Diego State University Computing Services Lines: 4 Message-ID: <3bbpfe$q7d@gondor.sdsu.edu> NNTP-Posting-Host: 130.191.1.100 X-Newsreader: TIN [version 1.2 PL0] Hi, I'm a PhD student (molecular biology) at San Diego State University I would like to know who else is surfing the net. My address is t1001@ucssun1.sdsu.edu From owner-embldatabank@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!TAWA.FRI.CRI.NZ!BISHOPS From: BISHOPS@TAWA.FRI.CRI.NZ (Sharon Bishop-Hurley) Newsgroups: bionet.molbio.embldatabank Subject: Re: what i'm doing in life Date: 29 Nov 1994 11:34:20 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net HI, saw your message on the bionet news and thought i would send you a message. My name is Sharon Bishop-Hurley and i have just recently started a PhD in molecular biology at New Zealand Forest Research Institute. My area of research is embryo development in radiata pine with the aim of isolating some embryo-specific genes. Keep cool sharon From owner-embldatabank@net.bio.net Tue Nov 29 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!uunet!newstf01.news.aol.com!newsbf01.news.aol.com!not-for-mail From: drrutledge@aol.com (Drrutledge) Newsgroups: bionet.molbio.embldatabank Subject: How do you download from genbank? Date: 29 Nov 1994 21:35:05 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 3 Sender: news@newsbf01.news.aol.com Message-ID: <3bgocp$r06@newsbf01.news.aol.com> NNTP-Posting-Host: newsbf01.news.aol.com What is the easiest way to download a sequence from genbank to then be used in the new Oligo for windows program? Should I be getting to genbank through world wide web (mosaic)? If so, what is the URL address? From owner-embldatabank@net.bio.net Tue Nov 29 22:00:00 1994 Path: biosci!BORDUAS.NLM.NIH.GOV!francis From: francis@BORDUAS.NLM.NIH.GOV (Francis Ouellette) Newsgroups: bionet.molbio.embldatabank Subject: Re: How do you download from genbank? Date: 29 Nov 1994 19:21:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411300321.AA08114@borduas.nlm.nih.gov> Reply-To: francis@ncbi.nlm.nih.gov NNTP-Posting-Host: net.bio.net > What is the easiest way to download a sequence from genbank to then be > used in the new Oligo for windows program? Should I be getting to genbank > through world wide web (mosaic)? If so, what is the URL address? The URL for GenBank is: http://www.ncbi.nlm.nih.gov regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov