NAME

AlignDB::DeltaG - Calculate deltaG of polymer DNA sequences

SYNOPSIS

Normal use

    use AlignDB::DeltaG
    my $deltaG = AlignDB::DeltaG->new(
        temperature => 37,
        salt_conc   => 1,
    );
    my $seq = "TAACAAGCAATGAGATAGAGAAAGAAATATATCCA";
    print "$seq deltaG: ", $deltaG->polymer_deltaG($seq), "\n";

Reset conditionss

    use AlignDB::DeltaG;
    # default value:
    #   temperature => 37,
    #   salt_conc   => 1,
    my $deltaG = AlignDB::DeltaG->new;
    $deltaG->temperature(30);
    $deltaG->salt_conc(0.1);
    $deltaG->BUILD;
    my $seq = "TAACAAGCAATGAGATAGAGAAAGAAATATATCCA";
    print "$seq deltaG: ", $deltaG->polymer_deltaG($seq), "\n";

DESCRIPTION

AlignDB::DeltaG is a simple class to calculate deltaG of polymer DNA sequences using the NN model.

In the near future, it may be extanded to calculate oligonucleotide thermodynamics.

Reference

 1. SantaLucia J, Jr. 2004. Annu Rev Biophys Biomol Struct;
 2. SantaLucia J, Jr. 1998. Proc Natl Acad Sci U S A;

ATTRIBUTES

temperature - default: 37.0 degree centigrade

salt_conc - salt concentration, Default: 1 [Na+], in M. Should be above 0.05 M and below 1.1 M

deltaH - enthalpy, isa HashRef

deltaS - entropy (cal/K.mol), isa HashRef

deltaG - free energy, isa HashRef

METHODS

BUILD

rebuild the object by the new temperature and/or salt_conc values

polymer_deltaG

    my $dG = $obj->polymer_deltaG($seq);

Calculate deltaG of a given sequence.

This method is the main calculating sub.

AUTHOR

Qiang Wang <wang-q@outlook.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2008 by Qiang Wang.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.