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

Perl module extract extract peptide sequences MEDLINE article abstracts peptide

Peptide::Pubmed Description

Peptide::Pubmed is a Perl module that can extract peptide sequences from MEDLINE article abstracts. 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, Author => q, Journal => q, Title => q, Abstract => q, Mesh => q, Chemical => q, }; $parser->parse_abstract($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 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 $word (@words) { # combined word/abstract score, in the interval print "$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, }; $parser->parse_abstract($in); @words = $parser->get_words; # No peptide sequences are found in empty input: $in = undef; $parser->parse_abstract($in); @words = $parser->get_words; Requirements: · Perl

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