[Bioperl-l] Running Smith Waterman alignments in BioPerl

[Chris Fields]

On Jul 22, 2010, at 9:41 AM, Peter wrote:

> On Thu, Jul 22, 2010 at 2:57 PM, Evelyne <evelyne.c88 at gmail.com> wrote:
>> 
>> Hi,
>> 
>> I would like to run a SW alignment, but i'm new to programming...
>> Tried using several tutorials to install this Bioperl-ext package, but not
>> getting that far...
>> Maybe you can help?
> 
> How about using the water tool in EMBOSS? I'm sure BioPerl has
> wrappers for that...
> 
> http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html
> 
> Peter

Yes, we do.  I would suggest that solution as well; the SW work in bioperl-ext hasn't been maintained actively for a while.  That doesn't mean it won't suit your needs, but issues with compilation will likely remained unaddressed.

chris