[Bioperl-l] Implementing standalone Smith Waterman analysis using BioPerl interfaces.

[Barry Moore]

Shachar-

The Bio::Factory::EMBOSS module has some documentation and happily for 
you the example they give is the for the program water which is a 
Smith-Waterman local alignment tool.

http://doc.bioperl.org/bioperl-run/Bio/Factory/EMBOSS.html

Barry

Shachar Zehavi wrote:

>Hello.
>
>This is a newbie question...
>
>I would like to implement a local Smith Waterman service and I don't really know which interfaces to use.
>
>I saw that both Bio::Tools::Run::StandAloneBlast  and Bio::Tools::Run::Alignment::StandAloneFasta
>inherit from Bio::Tools::Run::WrapperBase, but as far as I can understand some of the analysis running interface (parameters definition etc.) is defined in 
>Bio::AnalysisI interface.
>
>Is there a good example I can look at and learn from?
>
>Thanks in advance,
>Shachar.
>
>Shachar Zehavi
>Computational Medicine Infrastructure Team leader,
>Compugen Ltd.
>72 Pinchas Rosen, Tel Aviv 69512, Israel
>------------------------------------
>Tel: +972-3-765-8585
>Direct: +44-(115)-877-0971 or +972-3-765-8543
>Mobile: +44-(786)-791-2048
>Fax: +972-3-765-8555
>E-mail: shachar at compugen.co.il
>Website: http://www.cgen.com
>
> 
> <<Shachar Zehavi.vcf>> 
>  
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT