Free peptide software for linux

Peptide::Pubmed is a Perl module that can extract peptide sequences from MEDLINE article abstracts.

SYNOPSIS

use Peptide::Pubmed;
$parser = Peptide::Pubmed->new;
$in = {
PMID => q[15527327],
Author => q[Doe JJ, Smith Q],
Journal => q[J Biological Foo. 2004;8(2):123-30.],
Title => q[Foo, bar and its significance in phage display.],
Abstract =>
q[Peptide sequences EYHHYNK and Arg-Gly-Asp, but not ACCCGTNA or VEGFRI.],
Mesh => q[Genes, p53/genetics; Humans; Bar],
Chemical => q[Multienzyme Complexes; Peptide Library; Foo],
};
$parser->parse_abstract($in);

# get the peptide sequences in 1 letter symbols (select all words where the
# combined word/abstract score is above threshold:
# WordAbstScore >= WordAbstScoreMin):
@seqs = $parser->get_seqs;
print "@seqsn"; # prints: EYHHYNK RGD

EXAMPLES

# same as above, set threshold explicitly:
$parser->WordAbstScoreMin(0.4);
@seqs = $parser->get_seqs;

# set low threshold to get more peptide sequences (but at a cost of getting
# more false positives)
$parser->WordAbstScoreMin(-1);
@seqs = $parser->get_seqs;
print "@seqsn"; # prints: EYHHYNK RGD ACCCGTNA VEGFRI

# reset threshold back:
$parser->WordAbstScoreMin(0.4);

# get more data for the abstract:
$abst = $parser->get_abst;
print "$abst->{AbstScore}n"; # abstract score, in the [0,1] interval
print "$abst->{AbstMtext}n"; # abstract with sequences marked up:
# Peptide sequences EYHHYNK and Arg-Gly-Asp,
# but not ACCCGTNA or VEGFRI.

# get more data for the words, in addition to peptide sequences:
@words = $parser->get_words;
for my $word (@words) {
# combined word/abstract score, in the [0,1] interval
print "$word->{WordAbstScore}n";
# word as found in the abstract, eg Arg-Gly-Asp,
print "$word->{WordOrig}n";
# peptide sequence in 1 letter symbols, eg RGD
print "$word->{WordSequence}n";
}

# There are no mandatory input fields. This will work too, but may give lower score.
$in = {
Abstract =>
q[Peptide sequences EYHHYNK and Arg-Gly-Asp, but not ACCCGTNA or VEGFRI.],
};
$parser->parse_abstract($in);
@words = $parser->get_words;

# No peptide sequences are found in empty input:
$in = undef;
$parser->parse_abstract($in);
@words = $parser->get_words;

MassSpec::CUtilities is a Perl extension containing C utilities for use in mass spectrometry.

SYNOPSIS

MassSpec::CUtilities is an XS module so theres a chance that you or your target user might not get it to install cleanly on the target system; therefore its recommended to make its presence optional and to offer slower-performing Perl equivalents where practical.

Also note that this module uses a 19-letter amino alphabet rather than the traditional 20-letter alphabet, since the isobars Leucine(L) and Isoleucine(I) are represented instead by "X." Furthermore some portions of this module assume that their input peptides are internally in alphabetical order.

my $haveCUtilities;
if (eval require MassSpec::CUtilities) {
import MassSpec::CUtilities;
$haveCUtilities = 1;
} else {
$haveCUtilities = 0;
}
if ($haveCUtilities) {
my $candidate = MassSpec::CUtilities::encodeAsBitString("ACCGT");
my @shortPeptides = ("ACT","CCGM","ACCGTY","CCT");
my (@list,@answer);
foreach $_ (@shortPeptides) {
push @list, MassSpec::CUtilities::encodeAsBitString($_);
}
if (MassSpec::CUtilities::testManyBitStrings($candidate,@shortPeptides,@list,@answer)) {
# should print "ACT" and "CCT" only
print "Matched: " . join(,,@answer) . "n";
}
}

see API documentation for other available subroutines

ABSTRACT

An eclectic mix of C utilities originally used in a mass spectrometry denovo sequencing project at NIH. It includes a fast Huffman decoder suitable (with minor modifications) for use with the CPAN module Algorithm::Huffman, as well as a fast peptide mass calculator and methods for encoding peptides as products of prime numbers or as bitmaps.

An eclectic mix of C utilities originally used in a mass spectrometry denovo sequencing project at NIH. It includes a fast Huffman decoder suitable (with minor modifications) for use with the CPAN module Algorithm::Huffman, as well as a fast peptide mass calculator and methods for encoding peptides as products of prime numbers or as bitmaps.

MassCalculator is a Perl module that implements common mass computations in mass spectrometry.

SYNOPSIS

use InSilicoSpectro::InSilico::MassCalculator;
InSilicoSpectro::InSilico::MassCalculator::init(insilicodef.xml);

MassCalculator Perl library is intended to support common mass spectrometry-related computations that must be routinely performed by bioinformaticians dealing with mass spectrometry data.

To accommodate as many as possible user requirements, we decided to both support a classical procedural programming model and an object oriented model. Per se MassCalculator is not designed as an object oriented code but we provide a series of elementary classes for modeling proteins, peptides, enzymes, etc. which MassCalculator is compatible with. Moreover, the latter classes are rather simple and neutral in their design such that they should fit, after further derivations eventually, a large range of code design.

We decided not to use Perl object oriented programming to stay with relatively naive and simple code and to allow everybody to decide how to include it in its own project. Nonetheless, MassCalculator is able to deal with Perl objects we provide additionally to represent protein sequences, peptides, enzymes, mass lists, and fragmentation spectra, see their respective documentations.
MassCalculator is released under the LGPL license (see source code).