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

Shachar Zehavi shachar at compugen.co.il
Thu Aug 19 11:00:44 EDT 2004


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

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