Query: tfbs::word::consensus
OS: debian
Section: 3pm
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
TFBS::Word::Consensus(3pm) User Contributed Perl Documentation TFBS::Word::Consensus(3pm)NAMETFBS::Word - IUPAC DNA consensus word-based pattern class =head1 DESCRIPTION TFBS::Word is a base class consisting of universal constructor called by its subclasses (TFBS::Matrix::*), and word pattern manipulation methods that are independent of the word type. It is not meant to be instantiated itself.FEEDBACKPlease send bug reports and other comments to the author. AUTHOR - Boris Lenhard Boris Lenhard <Boris.Lenhard@cgb.ki.se>APPENDIXThe rest of the documentation details each of the object methods. Internal methods are preceded with an underscore. new Title : new Usage : my $pwm = TFBS::Matrix::PWM->new(%args) Function: constructor for the TFBS::Matrix::PWM object Returns : a new TFBS::Matrix::PWM object Args : # you must specify the -word argument: -word, # a strig consisting of letters in # IUPAC degenerate DNA alphabet # (any of ACGTSWKMPYBDHVN) ####### -name, # string, OPTIONAL -ID, # string, OPTIONAL -class, # string, OPTIONAL -tags # a hash reference reference, OPTIONAL search_seq Title : search_seq Usage : my $siteset = $pwm->search_seq(%args) Function: scans a nucleotide sequence with the pattern represented by the PWM Returns : a TFBS::SiteSet object Args : # you must specify either one of the following three: -file, # the name od a fasta file (single sequence) #or -seqobj # a Bio::Seq object # (more accurately, a Bio::PrimarySeqobject or a # subclass thereof) #or -seqstring # a string containing the sequence -max_mismatches, # number of allowed positions in the site that do # not match the consensus # OPTIONAL: default 0 search_aln Title : search_aln Usage : my $site_pair_set = $pwm->search_aln(%args) Function: Scans a pairwise alignment of nucleotide sequences with the pattern represented by the word: it reports only those hits that are present in equivalent positions of both sequences and exceed a specified threshold score in both, AND are found in regions of the alignment above the specified conservation cutoff value. Returns : a TFBS::SitePairSet object Args : # you must specify either one of the following three: -file, # the name of the alignment file in Clustal format #or -alignobj # a Bio::SimpleAlign object # (more accurately, a Bio::PrimarySeqobject or a # subclass thereof) #or -alignstring # a multi-line string containing the alignment # in clustal format ############# -max_mismatches, # number of allowed positions in the site that do # not match the consensus # OPTIONAL: default 0 -window, # size of the sliding window (inn nucleotides) # for calculating local conservation in the # alignment # OPTIONAL: default 50 -cutoff # conservation cutoff (%) for including the # region in the results of the pattern search # OPTIONAL: default "70%" to_PWM validate_word length perl v5.14.2 2008-01-24 TFBS::Word::Consensus(3pm)