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Screening of Yeast Protein Databases

Francis Ouellette francis at BORDUAS.NLM.NIH.GOV
Thu Feb 16 11:07:07 EST 1995


Bonjour Martine,

> We are interested in screening very recently updated Yeast Protein 
> Databases with a short amino acid sequence corresponding to a conserved 
> protein motif. Search of swissprot, PIR, PDB, etc. by Blast at NCBI 
> yielded several mammalian proteins, but none from S. cerevisiae.  Are 
> these banks updated frequently or are there other more frequently 
> updated sources (genome sequencing project) that one can access for such 
> a search?

The 'blastable' databases at NCBI are updated on a daily basis and
represents the latest version of what is in GenBank, EMBL and DDBJ.  We
(NCBI/GenBank) get updates from DDBJ and EMBL on a daily basis, and
build 'nr' ("non-redundant" databases) from these.  We build nr for
nucleotides and for proteins.  The protein 'nr' is non-redundant with
Swiss-prot, PIR (MIPS), PDB, GenPept (a CDS on a GenBank file which is
not in the protein databases yet) and updates from all of these.

Please note that we take a very stringent definition of 'nr' ... they
have to identical over their full length to be merged into one record.
A single nucleotide or aminoacid is enough to make you 'different'.

So if you blastn/p/x your sequence and you don't see a yeast hit, that
means it's probably not sequenced yet, or if it has, it hasn't been
released (made public) by the sequencing group.

Some yeast sequencing group release their sequenced data fasters than
others.

Hope all is clear, let me know otherwise,

regards,

francis


--
| B.F. Francis Ouellette  
|
| francis at ncbi.nlm.nih.gov   


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