[Bioperl-l] sequence proxy server

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Apr 16 17:28:11 EDT 2012

I assume you've done the obvious thing and tried downloading from your local mirror?
Or ours:

If you have a large number of requests it's almost always faster to download the refseq files and extract locally rather than run queries against NCBI via the web.


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Kevin Murray
> Sent: Saturday, 7 April 2012 1:50 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] sequence proxy server
> 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. One
> solution would be to use Bio::DB::Flat with GenBank sequences on a local
> computer. However, in a situation where there are multiple people in a lab
> doing bioinformatics, it seems to me a bit of a waste to have the entire
> genbank/genpept database, or even the relevant sections thereof, on each
> computer. So, i though about writing a "sequence proxy" cgi script, and a
> corresponding module, which would work a bit like this:
> The user calls Bio::DB::SeqProxy::GenBank as they would Bio::DB::GenBank,
> with the exception that a parameter for the address of the sequence proxy
> server is required.
> The module then sends a request similar to that sent to NCBI's servers  by
> calling Bio::DB::GenBank->get_Seq_by_x() to the sequence proxy server I
> believe all requests go to the efetch page now (please correct me if I'm
> wrong, i have read the relevant bioperl module code but not thoroughly), so
> the CGI script on the sequence proxy would take arguments in a similar
> fashion to make writing the client side module easier.
> The CGI script would use a Bio::DB::Flat database, or an interface to an SQL
> database to determine if the required sequence is stored locally. (as a aside,
> i'd like your thoughts on Bio::DB::Flat vs Bio::DB::Sql or similar) If the
> sequence exists locally, it would be returned to the user, either as plain text,
> or inside an XML container (see below).
> If not, it would be retrieved from the remote database using the relevant
> Bio::DB module, and returned.
> The sequence would either be returned as the relevant sequence format
> (which would default to GenBank format) in plain text, or as an XML
> document similar to:
> <result>
> <successful>1</successful>
> <sequence>___YOUR GENBANK FILE HERE___</sequence> <source>Local
> Database</source> </result> The aim of the xml document would be to
> simplify handling of server errors and allow for the specification of other
> metadata such as which database the sequence came from.
> Firstly, I'd like to know if this sounds feasible, and if so, if someone is already
> working on something similar? I don't want to reinvent the wheel.
> Secondly, I'd like to ask for your comments and advice. Being reasonably new
> to bioperl (started using bioperl about 6 months ago, but I've been coding in
> various languages for 8 years) I don't expect to have considered things that
> may seem obvious to a more experienced bioperl-er, so please be as brutally
> constructive in your criticism as you see fit =].
> I know this is alot of questions, so thanks in advance for your help.
> Cheers, and a happy Easter to those who celebrate it.
> Regards
> Kevin Murray
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