Bio::Tools::Solubility::Wilkinson - Calculate the probability of a protein to be soluble using the Wilkinson-Harrison model
version 0.093360
use Bio::Tools::Solubility::Wilkinson; my $seq = 'MMAEELLVIKP...'; my $s = solubility($seq);
This module implements a simple method for the prediction of protein solubility, as described by Wilkinson, D.L. and Harrison [1] and modified by Davis [2]. It only takes the primary sequence of the protein as a parameter, and returns the calculated probability that the protein will be expressed in soluble form in E. Coli.
It uses aminoacid composition to compute the two main parameters found to have strong correlation with solubility: charge average and turn forming residue fraction. For a detailed description of the formula used, check the article by Harrison [3] in the References section.
Returns the probability of the sequence $seq being soluble. $seq should be a correct and validated protein sequence written in one-letter aminoacid code. Any whitespace (spaces, newlines, tabs, etc) will be ignored.
$seq
my $probability = solubility($seq);
This function is exported by default.
If you'd like to rename the only imported subroutine for some reason, you can do:
use Bio::Tools::Solubility::Wilkinson solubility => { -as => 'solubility_wilkinson' }; use Some::Other::Solubility::Module 'solubility_foo'; my $p1 = solubility_wilkinson($seq); my $p2 = solubility_foo($seq);
This (and other goodies) are possible thanks to Sub::Exporter, which is worth checking out.
[1] Wilkinson, D.L. and Harrison, R.G. (1991). Predicting the solubility of recombinant proteins in Escherichia coli BioTechnology 9, 443-448.
[2] Gregory D. Davis, Claude Elisee, Denton M. Newham, Roger G. Harrison (1999). New fusion protein systems designed to give soluble expression in Escherichia coli. Biotechnology and Bioengineering Volume 65 Issue 4, Pages 382 - 388
[3] R.G. Harrison. 2000. Expression of soluble heterologous proteins via fusion with NusA protein. inNovations. 11:4-7. http://www.biotech.ou.edu/innovations.pdf
Bruno Vecchi <vecchi.b gmail.com>
This software is copyright (c) 2009 by Bruno Vecchi.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install Bio::Tools::Solubility::Wilkinson, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Tools::Solubility::Wilkinson
CPAN shell
perl -MCPAN -e shell install Bio::Tools::Solubility::Wilkinson
For more information on module installation, please visit the detailed CPAN module installation guide.