Linux Certif

Toute la documentation sur la certification Linux LPI

TFBS::Word::Consensus.3pm

NAME

TFBS::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.

FEEDBACK

Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

Boris Lenhard <Boris.Lenhard@cgb.ki.se>

APPENDIX

The 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