[Bioperl-l] Running Smith Waterman alignments in BioPerl

Peter biopython at maubp.freeserve.co.uk
Thu Jul 22 11:42:25 EDT 2010

On Thu, Jul 22, 2010 at 4:21 PM, Evelyne <evelyne.c88 at gmail.com> wrote:
> I have really no idea what that means...
> Studying first year of bio-informatics, and have to make a small perl
> program as exam
> Maybe I'm in a bit over my head, I'll ask the tutor for some advice...

The EMBOSS project is a collection of open source command line
tools written in C, and includes a tool called "water" for doing Smith
Waterman (SW) sequence alignments. I was suggesting you could
use BioPerl to call this needle program and parse its output.

However, it sounds like you actually have a programming assignment
where the point is to actually implement the SW algorithm yourself (in
perl). In this case, EMBOSS won't be useful after all.


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