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资源说明：Profile-constrained sequence optimization using evolutionary algorithms
Evolver
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Profile-constrained protein sequence optimization using evolutionary algorithms
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### Introduction
Evolver is a module that makes it easy to optimize protein
sequences using any arbitrary function but retaining its similarity with
a given protein family.
It uses a fast, memory efficient and highly configurable
[Genetic Algorithms engine][1] suitable for long sequence inputs and both
high population and generation numbers.
Similarity with the input profile/alignment is calculated using any of
the currently available plugins. Chief among these is Hmmer, which uses
[Hidden Markov Models][2] to describe the protein family and emit an
e-value based score for each individual in the population. However, the
user can also choose simpler methods, incluiding a pure perl
implementation of the Needleman sequence alignment algorithm. The
pluggable architecture of the profile score module makes it easy to
modify, extend or turn off completely.
### Dependencies
This module is dependency-heavy. The most important, and their uses, are:
- **BioPerl and third-party executables**.
This module makes heavy use of [BioPerl][3], specially the
Bio::Tools::Run, Bio::SeqIO, Bio::Seq, Bio::AlignIO and
Bio::SimpleAlign namespaces. Aditionally, the user should have
installed standalone [Clustalw][4] and [Hmmer][3], both of which can
be obtained freely from their respective websites.
- **AI::Genetic::Pro::Macromolecule**
The GA engine, based on Lukaz's [AI::Genetic::Pro][5].
- **Moose and friends**
Finally, this module uses [Moose][6], a postmodern OO system for
Perl. It also makes deliberate use of some MooseX extensions,
notably [MooseX::Object::Pluggable][7].
INSTALLATION
To install this module, run the following commands:
perl Makefile.PL
make
make test
make install
SUPPORT AND DOCUMENTATION
After installing, you can find documentation for this module with the
perldoc command.
perldoc Evolver
COPYRIGHT AND LICENCE
Copyright (C) 2009 Bruno Vecchi
This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
[1]: http://search.cpan.org/~strzelec/AI-Genetic-Pro-0.335/lib/AI/Genetic/Pro.pm "AI::Genetic::Pro"
[2]: http://hmmer.janelia.org/ "Hmmer"
[3]: http://www.bioperl.org/ "BioPerl"
[4]: http://www.ebi.ac.uk/Tools/clustalw2/index.html "Clustalw"
[5]: http://search.cpan.org/~strzelec/AI-Genetic-Pro-0.335/lib/AI/Genetic/Pro.pm "AI::Genetic::Pro"
[6]: http://www.iinteractive.com/moose/ "Moose"
[7]: http://search.cpan.org/~groditi/MooseX-Object-Pluggable-0.0009/lib/MooseX/Object/Pluggable.pm "M::O::Pluggable"
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