[Bioperl-l] Slow restriction digestion

[anthony.underwood at hpa.org.uk]

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?


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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