[Bioperl-l] Client-side Scansite Bioperl module

Chris Fields cjfields at illinois.edu
Mon Sep 27 17:07:11 EDT 2010


Sorry, didn't see this being responded to on-list (been off the radar the last month).  I think this is a good idea, but I'm wondering if this might be better as a separate release on CPAN from bioperl core, seeing as we're in the prelim stages after the next bioperl release of modularizing the current bioperl core into smaller independent releases.

chris

On Sep 4, 2010, at 10:40 AM, Jonathan Rameseder wrote:

> hi guys
> 
> it seems Bioperl contains a wrapper [1] for Scansite [2]. in what extent would it make sense to integrate a client-sided version of Scansite with some statistical analysis features (eg enrichment tests) in Bioperl? that would give users the opportunity to customize their own version of the Scansite algorithm. i developed an object-oriented client-sided version and am currently writing test cases.  maybe it could be integrated with the server wrapper somehow? please let me know what you think :-D!
> 
> best wishes
> johnny
> 
> [1] Bio::Tools::Analysis::Protein::Scansite
> [2] http://www.ncbi.nlm.nih.gov/pubmed/11283593
> 
> ********************
> Jonathan Rameseder
> Ph.D. Candidate
> Computational Systems Biology Initiative
> Koch Institute for Integrative Cancer Research
> Massachusetts Institute of Technology
> ********************




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