[Bioperl-l] Pairwise seq. comarison

[Barry Moore]

Bio::Align::PairwiseStatistics has a method "number_of_differences".  I 
haven't used it, but I presume you'd use AlingIO to bring in you 
alingment, and then just call the "number_of_differences" directly on 
your Bio::Align::AlignI  object.  The docs look kind of vauge, so 
hopefully someone else can flesh out this suggestions, but if your just 
looking for where to start experimenting, that's one place to try.

Barry

henrik nilsson wrote:

>Hi,
>
>For two aligned (and obviously overlapping) sequences, can I use Bioperl to 
>retrieve the number of differing sites in the alignment (for the overlapping 
>region only, excluding the flanking regions where only one of the two 
>sequences is present)?
>
>Thanks,
>
>RN
>
>
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-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT