Yeasties PomBase Database pombase
Thu Feb 15 06:42:01 EST 1996


************************* PomBase *****************************
************* A Schizosaccharomyces pombe database ************

A new compilation of S. pombe data in ACEDB for UNIX computers 
is now available by anonymous FTP (see below)

This release of PomBase (4-1) marks a change in the way that PomBase is
curated and distributed. PomBase will be completely rebuilt from ace
files at the Sanger Centre at each release. Old versions of PomBase
should be dicarded and the latest release downloaded by ftp.
Although this will require longer ftp jobs it has several advantages.
Curation time is reduced to a minimum and therefore releases can be
more frequent. It also allows models and database code to be updated
frequently without significant interactions by users. 

PomBase now includes:


Release 19.0 (November 1995) of the ENZYME database 


Release 13.0 (November 1995) of the Prosite Pattern Database 

* Genetic maps

Munz, P., Wolf, K., Kohli, J. and Leupold U. (1989). Genetics
overview in Nasim A. et al. (Eds), Molecular Biology of the fission
yeast, Academic Press, London, pp. 1-30

* Physical Maps

Updated views of the ICRF physical maps (Hoheisel, J. et al. 1993) and
correlations with the restriction fingerprinting maps from the Sanger
Centre. A new map "Sanger_I" shows the production status of cosmids
undergoing sequencing.

Hoheisel, J. et al., (1993). High Resolution Cosmid and P1 Maps
Spanning the 14Mb genome of the fission yeast S. pombe. Cell 73,

* DNA sequences

644 DNA sequences from EMBL and EMNEW including 38 cosmid sequences
from systematic genome sequencing projects. All cosmids have the
results of BLASTN and BLASTX searches of the EMBL/EMNEW and SWIR
databases respectively (Note. SWIR is a non-redunadant compliation of
SWISS-PROT, PIR and WORMPEP). Most cosmids also have the results of a
TBLASTX search of the dbEST database.

The Blixem tool on the sequence display now works for BLASTX. Pick a
BLASTX homology block (light blue) with the right hand mouse button to
reveal a menu; choose "Analyse in Blixem". This will give a multiple
alignment of peptide sequences to a 3 phase translation of the query
* Papers

1983 references to papers

* Protein records

1041 full text records of S. pombe peptides from SWISSPROT and PIR
4182 peptides showing homology to S. pombe proteins

* Gene Designations

378 new gene predictions from the Sanger Centre's chromosome I
sequencing project

1113 known S. pombe genes


Get PomBase by anonymous FTP from:

ftp.sanger.ac.uk in directory pub/PomBase/

README          This file
NOTES           Further notes - please get and read this file unless
                        you know exactly what you want to do.
INSTALL         The installation script 
ace4/           Subdirectory with binaries and source files
spombe/         Subdirectory with S. pombe ace files

doc/            Subdirectory containing documentation

Information about PomBase can be obtained from the Sanger Centre Yeast 
pages http://www.sanger.ac.uk/yeast/data.html


PomBase produced and curated by,

Sean Walsh, Marie-Adele Rajandream and Bart Barrell
The Sanger Centre, Hinxton Hall, Hinxton, Cambridge CB10 1RQ
tel: 01223 494955 fax: 01223 494919

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