[BiO BB] NCBI web service
ethan.strauss at promega.com
Tue Sep 19 16:02:42 EDT 2006
I have figured out part of my problem, but not how to fix it...
What is happening is that I am running blast and just grabbing
gi numbers from the XML blast results. When I send these gi numbers to
NCBI, it sends me back all the data associated with each gi number. This
data includes the sequence. It turns out that a few of the gi numbers in
my test set point to complete chromosomes! I think that NCBI is
returning the information completely, but that the connection can't
support the many millions of characters being passed.
What I would like to do is somehow query just for the size of
the sequences being returned and not asked for info on sequences which
are too large. I have not dug through NCBI's documentation in great
depth yet, but a quick look turns up nothing. If anyone knows how to do
this already, I would appreciated it.
bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformatics.org
[mailto:bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformat
ics.org] On Behalf Of Ethan Strauss
Sent: Tuesday, September 19, 2006 11:05 AM
To: General Forum at Bioinformatics.Org
Subject: [BiO BB] NCBI web service
I have been using the NCBI eutils web service from a C#
application to automatically retrieve additional information (species,
links to the Gene db etc) about BLAST hits from the gi numbers. This
works when it works, but I have been having a lot of trouble with the
web service. It is slow and frequently I get Web service errors (The
underlying connection was closed: An unexpected error occurred on a
send) which seem to related to timeout and proxies and keepalive and
other stuff I don't really understand.
Anyway, Is there another web service that I might use to get the
same sorts of information from gi numbers or accession numbers? I need
to get species and associations with the gene database. If you know how
to get the NCBI service to work better for me, that would be good too. I
would like to get the full description line, but could live without it.
It is important for this application that I can get the info from a web
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