staffan at biochem.kth.se
Wed Nov 1 16:23:19 EST 1995
Stockholm & Paris November 1, 1995
The ninth 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
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 4-9:
* We are now using version 4.1 of of the database manager, ACEDB. Versions
exist for Unix/X11 and Macintosh. A complete package with the Macintosh
application and a preloaded database is available. Update files for
version 3.0 of the database manager are also available (this support will
be discontinued in the near future). Ace 4.1 has the following new
o Less diskspace needed for the database (size is roughly halved -
MycDB 4-9 takes about 25MB of diskspace, compared to 40MB for MycDB
o Faster display of large KeySets, due to presorting of keys.
o Blixem, the alignment display, is now fully integrated in AceDB.
MycDB 4-9 contains blastn alignments for all sequences in MycDB
against MycDB itself. With the correct external script, it will also
fetch sequences not present in the database from an external source.
A script for doing this is included, in the wscripts directory. At
present, MycDb only contains blastp data for a few sequences.
o The Map display is now customizable to a great degree, both
regarding the look and what objects to display.
o A new, WorldWideWeb-based, help system. This also requires an
external script. The old help system is still there, as a backup.
* New and edited sequences from EMBL/GenBank/DDBJ, current as of Oct 30,
1995. The number of Sequence objects is now 3234, of which 2891 are
nucleotide sequences, and 343 Protein sequences. 591 of the nucleotide
sequences contain DNA (the others are subsequences in some form or Peptide
sequences). The total amount of sequence is now 2,238,856 nt, an increase
of more than 43%. Most of this is due to the inclusion of a number of new
cosmid sequences from M. leprae.
Blastn searches have been performed on all the sequences in the database,
against the complete database itself. This data is included. The data can
be visualized with the Blixem tool.
* The number of literature citations have increased with 263. Included are
citations from MedLine, current up to Oct 4, 1995. The references for
sequences have been cleaned up to remove redundancies.
* The Locus class now includes some information on the function of the
products. In the future this information will move to a new Protein class
(for those products that are proteins).
* The webserver has a new sequence search facility, where you can make a
blast search on all the sequences in MycDB or on strain-specific subsets
for M.leprae, M.tuberculosis complex or M.smegmatis. The fasta files used
for these searches are also available from the ftp site.
For information on earlier releases, see the file MycDB.3-8.Release.txt.
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
(188.8.131.52) in pub/MycDB
* the ftp server at Institut Pasteur: ftp.pasteur.fr (184.108.40.206) in
* or the mirror site at the Weizmann Institute in Israel (thanks Jaime!):
bioinformatics.weizmann.ac.il (220.127.116.11) in pub/databases/acedb/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.
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
Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris
Cedex 15, France
Email: stcole at pasteur.fr
Fax: (33 1) 18.104.22.168
Voice: (33 1) 22.214.171.124
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