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

[Shachar Zehavi]

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
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E-mail: shachar at compugen.co.il
Website: http://www.cgen.com

 
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