[Bioperl-l] sequence proxy server

Peter Cock p.j.a.cock at googlemail.com
Tue Apr 10 16:07:28 EDT 2012


On Fri, Apr 6, 2012 at 2:49 PM, Kevin Murray <k.d.murray.91 at gmail.com> wrote:
> Hi all,
>
> I'm an undergrad student in molecular biology at the ANU in Australia,
> and my research projects are becoming increasingly bioinformatics
> heavy. The latest one has involved quite a large amount of sequence
> retrieval from GenBank and GenPept. The download speed to Australia
> from NCBI's servers is rather slow, and i've been thinking about how
> we can improve this. ...So, i though about writing a "sequence proxy" ...

Have you tried TogoWS? It is based Japan and offers access to
some of the local databases but also proxies some important
EMBL/EBI and NCBI resources as well - including GenBank.
I would expect you'd get much faster response times from
Australia than talking directly to the NCBI.
http://togows.dbcls.jp/site/en/rest.html

I think the TogoWS REST API is very nice to use, and seems to
give much clearer error messages than the NCBI Entrez site
(TogoWS uses HTTP error codes pretty consistently).

Biopython 1.59 onwards has a simple API for the TogoWS
REST interface, but their URL structure is very easy, so for
a simple one off task you can easily roll your own in Perl
(or write one for BioPerl?).

Peter


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