Retrieving arbitrary sequences with web services
I dig SOAP (once it's been abstracted out for me by a helper library: maybe I should say that I dig SOAP::Lite). It's good to see that bioinformatics centres are providing web service interfaces to their data.
One thing, though - quite often I want to retrieve DNA sequences that aren't centered around genes (gene-centric genomics? how very last century). And that's strangely difficult with existing bioinformatics web services (it's easy enough with the Ensembl API or with wget and the right URL for UCSC, but not quick).
For some reason they're all based around retrieving sequences by identifier, a la RefSeq. Doesn't seem much good if you're not looking at a feature already defined somewhere. What I'd really like to see is a server which takes in SOAP requests (or, even simpler, uses REST). It'd take four parameters:
Does such a server already exist? If not, why not?
One thing, though - quite often I want to retrieve DNA sequences that aren't centered around genes (gene-centric genomics? how very last century). And that's strangely difficult with existing bioinformatics web services (it's easy enough with the Ensembl API or with wget and the right URL for UCSC, but not quick).
For some reason they're all based around retrieving sequences by identifier, a la RefSeq. Doesn't seem much good if you're not looking at a feature already defined somewhere. What I'd really like to see is a server which takes in SOAP requests (or, even simpler, uses REST). It'd take four parameters:
- Build
- Chr
- Start
- End
Does such a server already exist? If not, why not?
posted by Stew @ 10:29 AM
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