PomBase release 4-3

Valerie Wood val at sanger.ac.uk
Mon Nov 3 23:53:47 EST 1997


*************************** PomBase ***************************
izosaccharomycespombeschizosaccharomycespombeschizosaccharomyce
spombeschizosaccharomycespombeschizosaccharomycespombeschizosac
charomycespombeschizosaccharomycespombeschizosaccharomycespombe
schizosaccharomycespombeschizosaccharomycespombeschizosaccharom
ycespombeschizosaccharomycespombeschizosaccharomycespombeschizo
************* 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 (4-3) has been completely rebuilt from ace
files at the Sanger Centre. Old versions of PomBase
should be dicarded and the latest release downloaded by ftp.

PomBase now includes:

* DNA SEQUENCES

1207 S. pombe DNA sequences from EMBL and EMNEW including 121 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-redundant compilation of
SWISS-PROT, PIR and WORMPEP). 


The sequence display incorporates the Blixem tool for BLASTX homology. 
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 sequence.
  
* PAPERS

4218 paper references, including abstracts

* PROTEIN RECORDS

1691 full text records of S. pombe proteins from SWISSPROT and TREMBL
16466 peptides showing homology to S. pombe proteins

* GENE DESIGNATIONS

~1280 new gene predictions from the sequencing project


* ENZYME

Release 21.0 (October 1996) of the ENZYME database 

* PROSITE

Release 13.0 (November 1995) of the Prosite Pattern Database 

* GENETIC MAPS

from:
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

Views of the ICRF physical maps (Hoheisel, J. et al. 1993) and
correlations with the restriction fingerprinting maps from the Sanger
Centre. A map "Sanger_I" shows the production status of maps 
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,
pp109-120




******************************************************************

Get PomBase by anonymous FTP from:

ftp.sanger.ac.uk in directory pub/PomBase/
(ftp://ftp.sanger.ac.uk/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 the Pombe sequencing project can be obtained from 
the Sanger Centre Pombe pages: 
http://www.sanger.ac.uk/Projects/S_pombe/

PomBase is also accessible via the HGMP-RC for registered users
running X-windows at:
http://www.hgmp.mrc.ac.uk/
under the Genome Databases menu


-----------------------------------------------------
                             | Valerie Wood    
   email: val at sanger.ac.uk   | The Sanger Centre
   tel: 01223 494954         | Wellcome Trust Genome Campus     
   fax: 01223 494919         | Hinxton	         
                             | Cambridge CB10 1SA         
-----------------------------------------------------





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