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

perl v5.10.1 2008-01-24 TFBS::Word::Consensus(3pm)