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MassSpec::CUtilities 0.04

  Date Added: January 25, 2010  |  Visits: 472

MassSpec::CUtilities

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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..

Requirements: No special requirements
Platforms: Linux
Keyword: Cutilities Fast Libraries Mass Massspec Massspeccutilities Module Perl Programming Utilities
Users rating: 0/10

License: Freeware Size: 16.38 KB
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