Peptide::Pubmed 1.02

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;.

Requirements:	No special requirements
Platforms:	Linux
Keyword:	Abstract,  Acccgtna,  Eyhhynk,  Medline,  Peptide,  Peptide Sequences,  Peptidepubmed,  Perl Module,  Print,  Rgd,  Sequences,  Wordabstscoremin,  Words
Users rating:	0/10