[Bioperl-l] module for finding restriction site in batch of sequences?

Brian Osborne osborne1 at optonline.net
Thu Feb 9 20:37:39 EST 2006


Claudia,

Yes, Bio::Restricion does this, see bptutorial.pl for code examples. Note
that statement "@fragments = $analysis->fragments($enzyme)". If the array
@fragments has more than 1 element that means your sequence has a site for
the enzyme in question.

Alternatively it sounds like you could use some kind of regular expression.

Brian O.


On 2/9/06 3:53 PM, "Lalancette, Claudia" <Lalancettec at agr.gc.ca> wrote:

> Greetings,
> 
>  
> 
> I need to find a way to look for a specific restriction enzyme site in
> hundreds of sequences.  Been looking at Bio::Restriction, but not sure
> if will work...  Any suggestions?
> 
>  
> 
> Thanks,
> 
> Claudia
> 
>  
> 
>  
> 
> 
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