[Bioperl-l] Nearly OT question(s) - across databases

[Sean Davis]

Elena,

By Stanford database, I assume you mean the Stanford SOURCE batch query web 
page?  If that is so, then you have already used the data available via 
Entrez.  SOURCE uses the unigene build from NCBI to map clones or genbank 
accessions to unigene and entrez gene.  In other words, using the entrez 
database will not help you get more information.  Unfortunately, it is not 
at all uncommon to have ESTs that do not map to a gene_id or unigene 
cluster, so those have to remain orphans.  This sounds like a 
microarray-type project, and if it is, what I tend to do is to find the ESTs 
that are "interesting" for followup and that are not annotated via other 
means and blast those against transcript libraries like refseq and ensembl 
transcripts to find the "best" match.  In some cases, this "best" match will 
not be very good, but in others it will be perfectly adequate to tell you 
what you are looking at.  So, in short, there are not other databases at 
NCBI that are likely to be helpful and your best bet is to blast the 
remaining ESTs against refseq for your genome of interest.

Sean

----- Original Message ----- 
From: <grassi.e at virgilio.it>
To: "Bioperl (E-mail)" <bioperl-l at bioperl.org>
Sent: Monday, January 24, 2005 6:55 AM
Subject: [Bioperl-l] Nearly OT question(s) - across databases


> Hello everybody,
>
> first of all I'd like to apologize for my poor english and the not very
> "bioperlic" question.
> I've got a list of ests from the stanford database and I need to obtain
> their unigene cluster and possibly gene-id (the stanford database doesn't
> supply this informations for all the ests).
> My question is: is there a quick way to do this using bioperl?
> I'd prefer to download the databases that are needed rather than 
> connecting
> to them remotely, because it would be too time-consuming.
> As long as I usually use plain perl I'm looking around the entrez gene 
> databases
> to understand the better way to gain the data that I need; but I was 
> wondering
> if using bioperl would help me.
>
> Thank you,
> Elena Grassi
>
>
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