[Bioperl-l] Running Smith Waterman alignments in BioPerl

Evelyne evelyne.c88 at gmail.com
Thu Jul 22 11:53:39 EDT 2010

There is actually no real assignment with a goal described.
We only have to prove that we understand and can use Perl.
(Description of the course states we are to learn the concepts of computer
and rudimentary Perl)

The Smith Waterman Tool was mentioned during the courses (along with BPlite,
and using remote and local BLASTs) so i wanted to explore this, without
really knowing how complicated the use of this could be...
Maybe they just wanted to let us know what possibilities there are, without
expecting that we could do this on our own...

Peter-329 wrote:
> 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.
> Peter
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