Re: SNP Analysis : Parser for Polybayes result

[i.j.nijman]

Hi,

Have you seen this page? There's a simple script which parses the
polybayes output.

Cheers,
Ies Nijman

Elango, Palchamy (ICRISAT-IN) wrote:

> I am using Polybayes program [Author: Prof. Gabor T. Marth] for SNP analysis.
>
> I wish to parse and extract SNP associated information from the output (textual mulitple sequence alignment) of Polybayes program.
>
> Alternatively I am trying out the possibilities of  converting the polybayes alignment output into any standard multiple alignment format, so that I can able to use other SNP analysis programs that read multiple sequence alignment files as input.
>
> I wish to use your parser script or any bioperl / biojava module.
> Does anyone know or use any bioperl /biopython /biojava module ?
> I shall be grateful if you could kindly provide me some tips or additional information on this.
>
> Thanking you
> Elango
> P.Elango
>
> GT-Biotechnology,
> International Crops Research Institute for the Semi-Arid Tropics (ICRISAT),
> Patancheru - 502 324, Andhra Pradesh, India.
> Work:  +(91) 40 307 13321 , Home: +(91) 40  559 98770 /  +(91) 98854 98770 (Mobile)
> pelango@... <mailto:pelango@...>   www.cgiar.org <http://www.cgiar.org>   elango@... <mailto:elango@...>

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[i.j.nijman]

forgotten link: http://www.ccgb.umn.edu/~lparsons/downloads/index.html
i.j.nijman@... wrote:

> Hi,
>
> Have you seen this page? There's a simple script which parses the
> polybayes output.
>
> Cheers,
> Ies Nijman
>
> Elango, Palchamy (ICRISAT-IN) wrote:
> > I am using Polybayes program [Author: Prof. Gabor T. Marth] for SNP analysis.
> >
> > I wish to parse and extract SNP associated information from the output (textual mulitple sequence alignment) of Polybayes program.
> >
> > Alternatively I am trying out the possibilities of  converting the polybayes alignment output into any standard multiple alignment format, so that I can able to use other SNP analysis programs that read multiple sequence alignment files as input.
> >
> > I wish to use your parser script or any bioperl / biojava module.
> > Does anyone know or use any bioperl /biopython /biojava module ?
> > I shall be grateful if you could kindly provide me some tips or additional information on this.
> >
> > Thanking you
> > Elango
> > P.Elango
> >
> > GT-Biotechnology,
> > International Crops Research Institute for the Semi-Arid Tropics (ICRISAT),
> > Patancheru - 502 324, Andhra Pradesh, India.
> > Work:  +(91) 40 307 13321 , Home: +(91) 40  559 98770 /  +(91) 98854 98770 (Mobile)
> > pelango@... <mailto:pelango@...>   www.cgiar.org <http://www.cgiar.org>   elango@... <mailto:elango@...>

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[lparsons]

Hello

I am the author of that web page, which is no longer up because the lab itself no longer exists.  

There should have been a redirect link back in 2006 when you wrote that message, however the redirect link itself would no longer work at this point.  I have attached the perl script that was mentioned in the link, feel free to use it however you like.  

I apologize for not getting this to you sooner, hopefully someone can make use of this old script.

SNP_analysis.pl

i.j.nijman wrote:

forgotten link: http://www.ccgb.umn.edu/~lparsons/downloads/index.html
[e-mail] wrote:
> Hi,
>
> Have you seen this page? There's a simple script which parses the
> polybayes output.
>
> Cheers,
> Ies Nijman
>
> Elango, Palchamy (ICRISAT-IN) wrote:
> > I am using Polybayes program [Author: Prof. Gabor T. Marth] for SNP analysis.
> >
> > I wish to parse and extract SNP associated information from the output (textual mulitple sequence alignment) of Polybayes program.
> >
> > Alternatively I am trying out the possibilities of  converting the polybayes alignment output into any standard multiple alignment format, so that I can able to use other SNP analysis programs that read multiple sequence alignment files as input.
> >
> > I wish to use your parser script or any bioperl / biojava module.
> > Does anyone know or use any bioperl /biopython /biojava module ?
> > I shall be grateful if you could kindly provide me some tips or additional information on this.
> >
> > Thanking you
> > Elango
> > P.Elango
> >
> > GT-Biotechnology,
> > International Crops Research Institute for the Semi-Arid Tropics (ICRISAT),
> > Patancheru - 502 324, Andhra Pradesh, India.
> > Work:  +(91) 40 307 13321 , Home: +(91) 40  559 98770 /  +(91) 98854 98770 (Mobile)
> > [e-mail] <mailto:[e-mail]>   www.cgiar.org <http://www.cgiar.org>   [e-mail] <mailto:[e-mail]>

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