[Bioperl-l] Slow restriction digestion

[Shawn Hoon]

On Tuesday, May 13, 2003, at 12:02  AM, anthony.underwood at hpa.org.uk  
wrote:

> Hi All,
>
>
> I'm trying to list all the MseI sites (recognition site TTAA)  in a 4
> megabase genome, using the Bio::Tools::RestrictionEnzyme module.
> This works but takes a VERY long time. Is there a way of speeding this  
> up?.
> I realise it maybe a perl string searching problem- since searching  
> long
> strings in perl tends to be slow and when I've written perl code to do  
> the
> same without Bio::Perl it is also very slow. Just wondered if there  
> were any
> neat tricks?
>
>


U might want to avoid using perl check out EMBOSS apps

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/ 
nucleic_restriction_group.html


hope that helps..

shawn


> Thanks,
>
> Anthony
>
> Dr Anthony Underwood
> Bioinformatics Unit
> Central Public Health Laboratory
> Health Protection Agency
> 61 Colindale Avenue
> London
> NW9 5HT
> t:    0208 2004400 ext. 3618
> f:    0208 3583138
> e: anthony.underwood at hpa.org.uk
>
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