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¶