[Bioperl-l] Checking molecular type for blast searches

[Jason Stajich]

In bioperl we guess it is DNA if the % of ATGC is > 85%. See
Bio::PrimarySeq method _guess_alphabet for an impementation of this.

I appreciate the need to catch these kinds of errors - but at some level
the user is going to have to be educated about what they are doing -
garbage in / garbage out.

On Thu, 18 Apr 2002, Andrew Hynes wrote:

> 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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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu