NAME

MS::PepUtils - utility functions for proteomics calculations

SYNOPSIS

    use MS::PepUtils qw/calc_mw calc_gravy calc_parker calc_aliphatic calc_fragments digest/;

    my $mw = calc_mw( 'ACDEF' );
    my $gravy = calc_gravy( 'ACDEF' );
    my $hydro = calc_parker( 'ACDEF' );
    my $ai = calc_aliphatic( 'ACDEF' );
    my @peps = digest(
        'ACDEF',
        ['trypsin'],
        0,
    );
    my @frags = calc_fragments(
        'ACDEF',
        [0, 0, 0, 0, 0, 0, 0],
        3,
        1,
    );

DESCRIPTION

WARNING: This module is deprecated. See below.

MS::PepUtils was a set of utility functions for common proteomics calculations. It's use has been superceded by the MS::Peptide and MS::Protein classes, which implement many of the same functions here in both OO and functional interfaces and are generally more useful. This module has been retained for backward-compatibility only.

FUNCTIONS

calc_mw

    my $mw = calc_mw( 'ACDEF' );

Returns the average molecular weight of a protein.

calc_gravy

calc_parker

    my $gravy = calc_gravy( 'ACDEF' );
    my $hydro = calc_parker( 'ACDEF' );

Returns calculation of average hydropathicity based on the GRAVY and Parker/Guo/Hodges scales, respectively.

calc_aliphatic

    my $ai = calc_aliphatic( 'ACDEF' );

Returns a calculation of aliphatic index for a protein.

digest

    my @peps = digest(
        'ACDEF',
        ['trypsin'],
        0,
    );

Performs an in silico hydrolytic cleavage of the protein sequence and returns an array of peptide sequences. Undocumented -- please use MS::Protein::digest in new code.

calc_fragments

    my @frags = calc_fragments(
        'ACDEF',
        [0, 0, 0, 0, 0, 0, 0],
        3,
        1,
    );

Returns a set of daughter fragment series representative of a fragmentation of a parental ion. The return value is an (undocumented) complex data structure. Please do not use in new code. The functionality will eventually be better implemented within other namespaces.

CAVEATS AND BUGS

Please report bugs to the author.

AUTHOR

Jeremy Volkening <jdv@base2bio.com>

COPYRIGHT AND LICENSE

Copyright 2016 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.