MycDB.4-22

Staffan Bergh staffan at sibirien.physchem.kth.se
Mon Dec 16 02:36:23 EST 1996


MycDB 4-22

Stockholm & Paris December 13, 1996

The 22nd release of the Mycobacterium database, MycDB, is now available.

MycDB is funded by the WHO and the Fondation Raoul Follereau and is
maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the
Institut Pasteur in Paris, France and the Department of Biochemistry at The
Royal Institute of Technology in Stockholm, Sweden.

MycDB is available free of charge via Internet network transfer. A complete
description of the procedure to retrieve and install the software and
database is available through the Internet (see MycDB.Retrieval).

MycDB is also available through the WorldWideWeb servers at the Royal
Institute of Technology (URL: http://www.biochem.kth.se/MycDB.html) and
(through the good offices of the Genome Informatics Group at the National
Agricultural Library) on the Agricultural Genome Information Server, AGIS,
in Beltsville, Maryland, USA (WorldWideWeb - URL:
http://probe.nalusda.gov:8300/other/index.html or gopher - URL:
gopher://probe.nalusda.gov:7000/11/genome.databases/mycdb/). Be aware that
it may take some time for the update to reach NAL.

MycDB uses the excellent database software written by Richard Durbin
(MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software
allows the user to browse information by simply pointing and clicking with
the workstation mouse. A variety of powerful query methods are also
available. However, our experience is that most users choose the mouse
interface to find the information they are interested in.

As far as possible all information is connected to other information in the
database. The database software presents the information in separate windows
that allow many parts of the database to be viewed at one time. There are
also many paths to any piece of information, allowing the user to easily
navigate the connections between the various types of information.

New in release 4-22:

   * Due to the amount of new data, this update comes as 9 files,
     update.myc.4-14.tar.Z to update.myc.4-22.tar.Z.
   * There is now a Windows 95/Windows NT version of the software. See the
     file MycDB.Retrieval for more info.
   * No model changes were made, but the method of keeping the database
     up-to-date has changed somewhat. Due to this some errors may have crept
     in, and the size of the update is somewhat inflated (but see below for
     the major reason for the size of this update). Please bear with us
     while we weed them out, the new curation scheme is intended to speed up
     the work with the database, and should shortly lead to more frequent
     updates.
   * The amount of sequence data is now: 17237 Sequence objects, of which
     1236 contain nucleotide sequences (DNA objects). Of these, 330 come
     from the M. tuberculosis/M. bovis cluster (total 2,414,443 nt), 78 from
     M. leprae (total 2,420,756 nt) and 53 from M. smegmatis (total 96,572
     nt). Total amount of sequence is 5,281,466 nt, an increase of 84.4%
     since last release. The largest contigous sequence is more than 201 kbp
     (MD0103). The great increase is due both to the M. tuberculosis
     sequencing efforts of Bart Barrell and his group at the Sanger Centre,
     and the group of Doug Smith at Genome Therapeutics (increase in M.
     tuberculosis sequences is 260%!), and to improved searching strategy
     for EMBL/GenBank.
     The coverage of EMBL/GenBank is current up to November 15.
     There are 5928 Peptide sequences, most of which are blastx hits from
     SwissProt. As earlier announced these will in the future move to a
     class of their own, with a special display.
   * There are 456 new Papers, from MedLine and from Sequence records,
     current up to November 5. The naming scheme for paper objects have
     changed, so that most papers now have names formed from their MedLine
     UID's (MEDLINE_xxxxxxxx).
   * The Colleague class has seen a substantial update, with the inclusion
     of the entire attendance list from this summer's Mycobact'96 conference
     in Stockholm.

For information on earlier releases, see MycDB.4-13.Release.txt.

The database currently requires a Unix workstation running X-Windows, a
Macintosh or a PC running Windows 95 or Windows NT. A variety of precompiled
versions of the ACEDB database software are available through anonymous ftp.
See the file MycDB.Retrieval.txt for more info.

If you have any questions, problems or comments please contact us, via
e-mail, fax, mail or telephone. If you are impatient and are already
familiar with internet/ftp, all relevant information can be found at

   * the WWW server at the Department of Biochemistry, KTH:
     http://www.biochem.kth.se/MycDB.html
   * the ftp server at the Department of Biochemistry, KTH:
     ftp.biochem.kth.se (130.237.52.64) in pub/MycDB
   * the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in
     pub/MycDB
   * the mirror site at the Weizmann Institute in Israel (thanks Jaime!):
     bioinformatics.weizmann.ac.il (132.76.55.12) in
     pub/databases/acedb/mycdb
   * or the mirror site at the Microbiology Dept., University of British
     Columbia in Canada (thanks Yossef!): cod.microbiology.ubc.ca
     (137.82.165.101) in pub/MycDB

The file MycDB.Retrieval.txt describes in more detail the database system
requirements, network retrieval procedures for obtaining the database and
methods of obtaining future updates.

For more information contact Staffan Bergh or Stewart Cole.

Staffan Bergh
Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden
Email: staffan at biochem.kth.se
Fax: (46 8) 24 54 52
Voice: (46 8) 790 9230

Stewart Cole
Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris
Cedex 15, France
Email: stcole at pasteur.fr
Fax: (33 1) 45.68.85.93
Voice: (33 1) 45.68.84.46
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/staffan
Last modified: Fri Dec 13 16:08:12 1996




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