[Bioperl-l] Parsing needle/water output

[shalabh sharma]

Thanks a lot, I really appreciate it.
-Shalabh

On Thu, May 14, 2009 at 5:41 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:

> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3
> A%3AAlignIO%3A%3Aemboss&sort_order=by+method&search_string=Bio%3A%3AAlig
> nio%3A%3Aemboss
>
> > -----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, May 14, 2009 1:14 PM
> > To: Scott Markel
> > Cc: bioperl-l
> > Subject: Re: [Bioperl-l] Parsing needle/water output
> >
> > 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
> > > Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
> > > 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> > > San Diego, CA 92121                 fax:    +1 858 799 5222
> > > USA                                 web:    http://www.accelrys.com
> > >
> > > http://www.linkedin.com/in/smarkel
> > > Vice President, Board of Directors:
> > >    International Society for Computational Biology
> > > Co-chair: ISCB Publications Committee
> > > Associate Editor: PLoS Computational Biology
> > > Editorial Board: Briefings in Bioinformatics
> > >
> > >
> > > > -----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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