[Bioperl-l] Implementing standalone Smith Waterman analysis using
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
>Is there a good example I can look at and learn from?
>Thanks in advance,
>Computational Medicine Infrastructure Team leader,
>72 Pinchas Rosen, Tel Aviv 69512, Israel
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>E-mail: shachar at compugen.co.il
> <<Shachar Zehavi.vcf>>
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