MycDB 4-12

Staffan Bergh staffan at biochem.kth.se
Tue Mar 26 22:58:06 EST 1996

MycDB 4-12

Stockholm & Paris March 26, 1996

The 12th 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.

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.

This release comes as three files, thus the jump in release numbers.

New in release 4-12:

   * Support for ace3 is discontinued as of this release. If you are
     absolutely unable to upgrade to ace4, contact Staffan.
   * The DraI/AsnI map of M. tuberculosis H37Rv. from Wolfgang Phillip and
     Stewart Cole, is now included. Locus positions will follow in a later
   * Annotation of the M. leprae cosmid sequences is somewhat more
     developed. All cosmid sequences now have the blastx matches against
     SwissProt included. These data are used for assigning function to
     orfs. The cosmids B26, B27, B32, B50, B650, B912, B937, B983, B1133,
     B1229 and BL308 have had their annotation updated. Two cosmid sequences
     have been added, B1770 and B1846.
   * The number of sequences have increased due to the breaking out of the
     peptide sequence data into separate objects (in general called
     'xxx_pepXX', where xxx is the nucleotide sequence it is derived from
     and XX is a counter). These as yet contain very little data, often only
     the accession number for the NCBI gene index database and/or the
     DDBJ/EMBL/GenBank PID accession numbers. The breaking out of these is
     in preparation for a major model change, the implementation of a
     Protein class with its own display.
   * The amount of sequence data is now: 9971 Sequence objects, of which 769
     contain nucleotide sequences (DNA objects). Of these, 212 come from the
     M. tuberculosis/M. bovis cluster (total 366,773 nt), 55 from M. leprae
     (total 1,678,065 nt) and 43 from M. smegmatis (63,711 nt). Total amount
     of sequence is 2,528,147 nt, an increase of 12.9% since last release.
     The coverage of EMBL/GenBank is current up to March 17. There are 2194
     Peptide sequences, of which slightly more than half are from
     mycobacteria (the rest are blastx hits from SwissProt).
   * There are 238 new Papers from MedLine, current up to March 8.
   * The webserver has gone through a complete overhaul and now has
     clickable images and a greatly improved query interface. (This was
     actually done in January, but no announcement has been made).
   * We now have a mirror site for the files at the University of British
     Columbia, thanks to Yossef Av-Gay.

For information on earlier releases, see the file MycDB.4-9.Release.txt at the
ftp sites.

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

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:
   * the ftp server at the Department of Biochemistry, KTH:
     ftp.biochem.kth.se ( in pub/MycDB
   * the ftp server at Institut Pasteur: ftp.pasteur.fr ( in
   * the mirror site at the Weizmann Institute in Israel (thanks Jaime!):
     bioinformatics.weizmann.ac.il ( in
   * or the mirror site at the Microbiology Dept., University of British
     Columbia in Canada (thanks Yossef!): cod.microbiology.ubc.ca
     ( 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)
Voice: (33 1)

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