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PomBase4-5

Valerie Wood val at sanger.ac.uk
Fri Dec 4 16:05:10 EST 1998


There is a new release of PomBase available for downloading at
ftp.sanger.ac.uk in directory pub/PomBase/
(ftp://ftp.sanger.ac.uk/pub/PomBase/)

PomBase is also accessible via the W.W.W at the HGMP-RC at 
http://www.hgmp.mrc.ac.uk/Registered/Option/pombase.html
(You may need to register when you first enter)

This release of PomBase (4-5) 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.
>From this release PomBase will be updated monthly.


PomBase now includes:


* PHYSICAL MAPS

*NEW* EUPOM physical maps showing the production status of cosmids 
undergoing sequencing. 

Views of the ICRF physical maps (Hoheisel et al 1993). 


* GENETIC MAPS

>From (Munz et al 1989).


* DNA SEQUENCES

9640 S. pombe DNA sequences from EMBL and EMNEW,
including 257 systematically sequenced cosmids (c.f. 121 release 4_4)
and the new est data from Mitsuoki Morimyo.

All sequenced cosmids have the results of BLASTN against fungi, 
TBLASTX searches against S. cerevisiae, and BLASTX against SWIR.
NOTE. SWIR is a non-redundant compilation of SWISS-PROT, TREMBL and 
WORMPEP). 

*NEW* est2genome has been used to map EST hits to the genomic 
sequences. These are shown as mauve homology blocks on the fmap.

*NOTE* The fmap (visual display for sequences) is now accessible
by clicking on the accession number under the DNA tag in the 
"Sequence" text window 


* PAPERS

4908 paper references, including abstracts


* PROTEIN RECORDS

~3300 full text records of S. pombe proteins from SWISSPROT and 
TREMBL


* GENE DESIGNATIONS

~2420 new gene predictions from the sequencing project

* LOCI

4674 loci and/or Synonyms


-----------------------------------------------------------------------
A new mailing list 'pombelist' has been set up at the Sanger Centre.

This mailing list is primarily to inform subscribers 
of developments and progress, of data and tools, relating to the S.
pombe Genome Sequencing project.

It will include periodic sequencing total updates, sequencing reports, 
details of new  releases and features of the S pombe database
POMBASE, and any other information which might be useful to the pombe
community.

To subscribe to the list people need to send mail to 

        majordomo at sanger.ac.uk

with the body of the message:-

subscribe pombelist
--



          **********           CONTACTS             *******

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


Please address
Sequencing enquiries to Marie-Adele Rajandream mar at sanger.ac.uk (Project
Manager)
Clone requests to Rhian Gwilliam rg1 at sanger.ac.uk (DNA co-ordinator)
Analysis and gene prediction queries to Mike Lyne mhl at sanger.ac.uk
                                     or Valerie Wood val at sanger.ac.uk
Pombase enquries to Valerie Wood val at sanger.ac.uk



-- 
----------------------------------------------------------------------------------
Valerie Wood		       Tel: 01223 494954
S. Pombe Genome Project	       Fax: 01223 494919 		       
The Sanger Centre              email: val at sanger.ac.uk
Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe 
Hinxton                        Preliminary Functional Classification: 
Cambridge                      http://www.sanger.ac.uk/Users/val/
CB10 1SA







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