mikechea/bioruby-protparam

A Protparam compatible utility for bioruby.

bio-protparam

bio-protparam adds Bio::Protparam class. Bio::Protparam has same interface and function as Bio::Tools::Protparam class of BioPerl, except that it calculate parameters instead of throwing query to Expasy protparam tool.

Note: this software is under active development!

Installation

    gem install bio-protparam

Usage

    require 'bio'
    require 'bio-protparam'
    
    protparam = Bio::Protparam.new("MYNNYNLCHIRTINWEEIITGPSAMYSYVY...")
    # Return Mw
    protparam.molecular_weight
    # Return pI
    protparam.theorettical_pI

To use Expasy's protparam, pass a ':remote' option to constructor.

    require 'bio'
    require 'bio-protparam'
    
    protparam = Bio::Protparam.new("MYNNYNLCHIRTINWEEIITGPSAMYSYVY...", :remote)
    # Return Mw
    protparam.molecular_weight
    # Return pI
    protparam.theorettical_pI

The API doc is on rdoc.info. For more code examples see the test files in the source tree.

Cite

If you use this software, please cite one of

• BioRuby: bioinformatics software for the Ruby programming language
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Biogems.info

This Biogem is published at #bio-protparam

Copyright

Copyright (c) 2012 hryk. See LICENSE.txt for further details.