[Bioperl-l] GeneDB Question

[Keith James]

>>>>> "Markus" == Markus Kador <markus at kador.de> writes:

    Markus> Hi, I would like to get sequence data form GeneDB
    Markus> (http://www.genedb.org/) in my perl script.  Since there
    Markus> is no module available I wanted to ask if anyone has ever
    Markus> done that or has any pointers on how to achive
    Markus> that. Specifically the blast server would be interesting.

As I'm at Sanger I've just been round to the genedb office to ask
about this.

I think that you will have to try screen-scraping the omniblast page
(rather than the individual organism blast pages). This way you can
search all the data but only have to maintain your script to mirror
the changes to one submission web page. However, that page is subject
to periodic changes in formatting and in the number and labelling of
radio buttons and checkboxes.

As you know, there is no public server or API. There is no likelihood
of these becoming available in the forseeable future, so a web-scraper
may be worth the effort.

I also asked about ftp availability of the data because I think that
if you have the resources (disk space & local blast) your best option
is to ftp the data to your local machine. Due to ongoing data-release
policy issues the ftp site data is not complete for some
organisms. You would need to contact the genedb people directly about
that.

HTH

Keith

-- 

- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -