[Bioperl-l] Parsing needle/water output

[shalabh sharma]

yes, i tried to read the documentation about Bio::AlignIO::emboss, but there
is not much in it.So is like i can call the same functions which are used in
searchIO. I need start and end position of the pairwise alignment.

Thanks
Shalabh


On Thu, May 14, 2009 at 3:58 PM, Scott Markel <SMarkel at accelrys.com> wrote:

> Shalabh,
>
> Have you looked at Bio::AlignIO::emboss?
>
> Scott
>
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> > Sent: Thursday, 14 May 2009 12:54 PM
> > To: bioperl-l
> > Subject: [Bioperl-l] Parsing needle/water output
> >
> > Hi All,
> >          Is there any parser/module available to parse needle/water
> output
> > report (from emboss) to get the start and end position of alignment.
> >
> > Thanks
> > Shalabh
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