yeast protein database?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Fri Jan 6 01:58:38 EST 1995


Arnoud Kal (KAL at AMC.UVA.NL) wrote:
: My questions are: how can I search NCBI and EMBL for 
: yeast proteins only? Are yeast protein databases available 
: that can be searched (preferably) via E-mail?

You might use the SRS system (Thure Etzold, EMBL) to generate 
a list of protein sequences with the organism name 'sacc*' - 
pereferably you might want to do this in the SWISSPROT database.
(currently, this gives you 2332 hits). However, as SWISSPROT
gives you the organism name as part of the entry ID, you would
already get a reasonably comprehensive set using swissprot:yeast*
(2286 hits). What you can do with SRS now is that you select 
all codon regions of the DNA database (e.g., in EMBL this is 
88434 etries, 94411 with updates) and 'map' the protein query on 
the DNA query. This gives you all CDS regions of sequences 
which are described as SWISSPROT entries in the protein database.
The 2534 entries can be searched as subset in FASTA or similar 
after extraction of the entry list on a local computer equipped
with the corresponding software (e.g., the GCG software allows 
searches with FASTA by FOSN files). 
SRS is on the world-wide web at http://www.embl-heidelberg.de/srs/srsc
and http://www.embl-heidelberg.de/srs/status.html gives you the 
current status of all 9 servers distributed world-wide. The 
package is available for local installation free of charge. 

You might want to inquire with the Dutch EMBnet node at CAOS/CAMM
in Niejmegen for an account so that you can use the system there 
for completing your query. If you use your account from locations
other than the Netherlands look up http://www.ch.embnet.org/embnet.news
in order to find one of the other 26 EMBnet nodes in Europe - the 
newsletters have a current list of nodes and access information as 
a listing, e.g. http://www.ch.embnet.org/embnet.news/vol1_2/item_9.html

Regards
Reinhard Doelz
Swiss EMBnet node 




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