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

Barry Moore barry.moore at genetics.utah.edu
Thu Aug 19 17:21:59 EDT 2004


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.



Shachar Zehavi wrote:

>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 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

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

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