[Bioperl-l] sequence proxy server

Fields, Christopher J cjfields at illinois.edu
Tue Apr 10 21:20:48 EDT 2012


On Apr 10, 2012, at 3:07 PM, Peter Cock wrote:

> 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

Should be easy enough if the API is well-documented.  

Related to this, anyone know if NCBI's REST API is documented anywhere?

chris




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