From owner-embldatabank@net.bio.net Sun May 02 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!huie From: huie@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: Processing of NCBI Backbone sequence data at EMBL Message-ID: <1993May3.142701.83812@embl-heidelberg.de> Date: 3 May 93 13:27:01 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 33 We will now include sequence data from the NCBI Backbone Database in the EMBL Nucleotide Sequence Database. The NCBI journal-scanning activity collects sequence data as published in scientific journals and builds the NCBI Backbone Database. However, most data these days is electronically submitted directly to one of the database groups at DDBJ, EMBL or GenBank. We have been careful to avoid data redundancy caused by adding data from the Backbone database for which their is a corresponding direct submission. Backbone data passes through a matching algorithm which uses combinations of the following criteria: . the accession number which is allocated to the data if it had already been directly submitted. If this is cited in the journal article, we find it in the Backbone entry. . same author name(s) . same organism . sequence similarity Backbone data which is determined to be novel or "unmatched" will be included in the EMBL Nucleotide Sequence Database, using the Backbone accession number (typically beginning with the letter 'S' at the moment), and with a dataclass of "backbone" indicated on the ID-line of the EMBL flat-file entry. Users may notice a different style of description text on the DE-line and the relative lack of annotation detail. The matching algorithm will be periodically re-applied to such data to catch the cases where a direct submission becomes available after a corresponding Backbone entry. Backbone data which already has a matching direct submission will not be included in the EMBL database proper, but will be retrievable via its Backbone database accession number via the EMBL e-mail file server. Other options for access will be considered. From owner-embldatabank@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: lukas.pellar@img.cas.cs Newsgroups: bionet.molbio.embldatabank Subject: no subject (file transmission) Message-ID: <1993May7.125934.14719@gserv1.dl.ac.uk> Date: 7 May 93 13:31:08 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 16 Content-Type: text Original-To: embl-db@uk.ac.daresbury X-Mailer: ELM [version 2.4 PL20] Content-Length: 709 HELP! My task is to create some representative collection of the human DNA repetitive sequences. I need the information about the genetic databases and libraries, where this sequences can be found, and the information about the tools, methods, programs , b Lukas Pellar UMG CAVR Flemingovo nam. 2 160 00 Praha 6 tel. 3312 346 From owner-embldatabank@net.bio.net Sun May 09 23:00:00 1993 Path: biosci!comp.bioz.unibas.ch From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.embldatabank Subject: Re: Direct Submissions to GenBank Message-ID: Date: 9 May 93 09:49:13 GMT References: <1993May7.173549.25001@nlm.nih.gov> Sender: kristoff@net.bio.net Organization: EMBnet Switzerland [Basel] Lines: 60 lipman@void.nlm.nih.gov (David Lipman) writes: ... >As part of these ongoing efforts, over the next year NCBI will be >assuming a larger role in the processing of direct author submissions >and updates. Beginning on May 17, 1993, direct submissions should be sent to >NCBI: > U.S. mail (for submissions on diskette, indicate whether Mac or PC): > GenBank Submissions > National Center for Biotechnology Information > Bldg. 38A, Room 8N-803 > 8600 Rockville Pike > Bethesda, MD 20894 > E-mail submission of new sequences: gb-sub@ncbi.nlm.nih.gov > E-mail submission of updates: update@ncbi.nlm.nih.gov > >NCBI and Los Alamos National Laboratory (LANL) have arranged to work >together to process direct submissions. Our goal is to continue to >enhance the value of the database through the direct contributions of >authors and, towards this end, we are developing new methods to submit >and update sequence information. We appreciate your input on how we >may improve the database and access to it. We invite you to send your >suggestions to 'info@ncbi.nlm.nih.gov'. Just to followup that other parts of the globe can also use the addresses quoted in the Appendix 2 of the EMBL data submission documentation. As far as I am informed, there is the commitment from all EMBL, DDBJ and GENBANK to collaborate on direct submissions - please correct me if this is not the case - and there should be any new GENBANK entry showing up in EMBL shortly after the submission, as was announced also to happen the other way round starting this week (i.e., the update files of GENBANK will include EMBL also.). EMBL Data Library: (a) Computer network: datasubs@EMBL-Heidelberg.DE (for data submissions); datalib@EMBL-Heidelberg.DE (for other enquiries) (b) Postal address: Data Submissions, EMBL Data Library, Postfach 10.2209, 6900 Heidelberg, Federal Republic of Germany (c) Telephone: +49-6221-387-258 (d) Telefax: +49-6221-387-519 (e) Telex: 461613 (embl d) DNA Databank of Japan (a) Computer network: ddbjsub@ddbj.nig.ac.jp (for data submissions); ddbj@ddbj.nig.ac.jp (for other enquiries) (b) Postal address: Laboratory of Genetic Information Analysis, Center for Genetic Information Research, National Institute of Genetics, Mishima, Shizuoka 411, Japan (c) Telephone: +81 559 75 0771 x647 (d) Telefax: +81 559 75 6040 -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | From owner-embldatabank@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!agate!spool.mu.edu!caen!nic.umass.edu!titan.ucs.umass.edu!not-for-mail From: lmegna@titan.ucs.umass.edu (Lisa Megna) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.gdb Subject: Database searching Message-ID: <1t88u8INNheo@titan.ucs.umass.edu> Date: 17 May 93 14:54:00 GMT Organization: University of Massachusetts - Amherst Lines: 9 Xref: biosci bionet.molbio.genbank:1296 bionet.molbio.embldatabank:179 bionet.molbio.gdb:69 NNTP-Posting-Host: titan.ucs.umass.edu How can I search these and other nucleotide and protein sequece databases by email? I am especially interested in searching databases not currently avaibale through gcg. For example, I have heard of a database of random sequences of human DNA. Thanks. Lisa Megna lmegna@titan.ucc.umass.edu From owner-embldatabank@net.bio.net Wed May 19 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rice From: rice@embl-heidelberg.de (Peter Rice) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.gdb Subject: Re: Database searching Message-ID: <1993May18.140336.85217@embl-heidelberg.de> Date: 18 May 93 13:03:36 GMT References: <1t88u8INNheo@titan.ucs.umass.edu> Organization: EMBL, European Molecular Biology Laboratory Lines: 43 Xref: biosci bionet.molbio.genbank:1299 bionet.molbio.embldatabank:180 bionet.molbio.gdb:70 In article <1t88u8INNheo@titan.ucs.umass.edu>, lmegna@titan.ucs.umass.edu (Lisa Megna) writes: > How can I search these and other nucleotide and protein sequece databases > by email? I am especially interested in searching databases not currently > avaibale through gcg. For example, I have heard of a database of random > sequences of human DNA. You have several options. The latest database entries are available at many sites for searching by E-mail. For example, you can send mail with the message text HELP to the following addresses: BLITZ@EMBL-Heidelberg.DE - massively parallel protein search program (like BESTFIT in GCG against the whole database) FASTA@EMBL-Heidelberg.DE - FASTA search of protein or DNA databases QUICK@EMBL-Heidelberg.DE - GCG QUICKSEARCH (improved version) other search services are regularly posted to these newsgroups, I expect you will get their details. BLAST services are especially useful. You should try both and compare them to BLITZ. As you have GCG you can also convert any other database to GCG format for searching. Sometimes you have to modify a GCG program or write a new one, but you have the full instructions with the package. Let me know if you need help with this. I assume the "random human DNA" database is a reference to EST sequencing efforts which aim to sequence a complete cDNA library. The "random" just means that a random cDNA is sequenced with no clue yet to its function. These sequences are already included in the EMBL/GenBank/DDBJ sequence databases, for human and for several other organisms. If there is sufficient demand, the EST sequences could be made available for searching separately by our search services - they are certainly "different" in that they may contain sequencing errors and their annotation is limited by the lack of biological knowledge. ----------------------------------------------------------------------------- Peter Rice, EMBL | Post: Computer Group | European Molecular Internet: Peter.Rice@EMBL-Heidelberg.DE | Biology Laboratory | Postfach 10-2209 Phone: +49-6221-387247 | W-6900 Heidelberg Fax: +49-6221-387306 | Germany From owner-embldatabank@net.bio.net Thu May 27 23:00:00 1993 Path: biosci!las!mbdmitry%ccvax.dnet From: mbdmitry%ccvax.dnet@las Newsgroups: bionet.molbio.embldatabank Subject: sequence information Message-ID: <9305290346.AA26236@las.as.edu.tw> Date: 29 May 93 03:46:30 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Dear Mrs: Would you please tell me how I can receive sequence of the lambda charon 4A vector left arm DNA from the position 18560 (Kpn1-site) to the position 20660 (Sac1-site of the lac-5 insert)? I would greately appreciate an answer. many thanks Dmitry Bessarab, Ph.D. Institute of Molecular Biology Academia Sinica Nankang, Taipei