[Bioperl-l] Checking molecular type for blast searches

[Andrew Hynes]

Hi All,

Please could someone point me in the direction of some code or strategies
for catching the molecular type of a sequence submitted for blast.  I want
to prevent users from sending the wrong sequence type to a blast algorithm
(e.g. submitting a protein seq to blastn). The Ensembl blast service warns
the user if they have submitted the wrong sequence type to a given
algorithm - how is this done?  My current strategy is to create a perl cgi
script that gathers blast paramaters from the user and passes them via
bioperl objects to StandAloneBlast with subsequent parsing.  I suspect that
this may be re-inventing the wheel - are there any standard blast cgi
interfaces (Bioperl?) that collect the blast parameters and do the error
checking?

Thanks for your help,

Andrew

Andrew M Hynes PhD
Bioinformatician
Software Engineering
Oxford GlycoSciences
The Forum
86 Milton Park
Abingdon
Oxon OX14 4RY
01235 208065


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