Visit Our UNIX and Linux User Community

Linux and UNIX Man Pages

Test Your Knowledge in Computers #305
Difficulty: Easy
A regular expression is an integer array that can be used to describe several sequences of characters.
True or False?
Linux & Unix Commands - Search Man Pages

tfbs::sitepairset(3pm) [debian man page]

TFBS::SitePairSet(3pm)					User Contributed Perl Documentation				    TFBS::SitePairSet(3pm)

NAME
TFBS::SitePairSet - a set of TFBS::SitePair objects SYNOPSIS
my $site_pair_set = TFBS::SitePairSet->new(@list_of_site_pair_objects); # add a TFBS::SitePair object to set: $site_pair_set->add_site_pair($site_pair_obj); # append another TFBS::SitePairSet contents: $site_pair_set->add_site_pair_set($site_pair_obj); # create an iterator: my $it = $site_pair_set->Iterator(-sort_by => 'start'); DESCRIPTION
TFBS::SitePairSet is an aggregate class that contains a collection of TFBS::SitePair objects. It can be created anew and filled with TFBS::Site::Pair object. It is also returned by search_aln() method call of TFBS::PatternI subclasses (e.g. TFBS::Matrix::PWM). 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. size Title : size Usage : my $size = $sitepairset->size() Function: returns a number of TFBS::SitePair objects contained in the set Returns : a scalar (integer) Args : none add_site_pair Title : add_site_pair Usage : $sitepairset->add_site_pair($site_pair_object) $sitepairset->add_site_pair(@list_of_site_pair_objects) Function: adds TFBS::SitePair objects to an existing TFBS::SitePairSet object Returns : $sitepairset object (usually ignored) Args : A list of TFBS::SitePair objects to add add_site_pair_set Title : add_site_pair_set Usage : $sitepairset->add_site_pair_set($site_pair_set_object) $sitepairset->add_site_pair(@list_of_site_pair_set_objects) Function: adds the contents of other TFBS::SitePairSet objects to an existing TFBS::SitePairSet object Returns : $sitepairset object (usually ignored) Args : A list of TFBS::SitePairSet objects whose contents should be added to $sitepairset Iterator Title : Iterator Usage : my $it = $sitepairset->Iterator(-sort_by=>'start'); while (my $site_pair = $it->next()) { #... Function: Returns an iterator object, used to iterate thorugh elements (TFBS::SitePair objects) Returns : a TFBS::_Iterator object Args : -sort_by # optional - currently it accepts # (default sort order in parenthetse) # 'name' (pattern name, alphabetically) # 'ID' (pattern/matrix ID, alphabetically) # 'start' (site start in sequence, # numerically,increasing order) # 'end' (site end in sequence, # numerically, increasing order) # 'score' (1st site in pair, # numerically, decreasing order) -reverse # optional - reverses the default sorting order if true set1 set2 Title : set1 set2 Usage : my $siteset1 = $sitepairset->set1(); : my $siteset2 = $sitepairset->set2() Function: Returns individual TFBS::SiteSet objects, from the site set pair Returns : A TFBS::SiteSet object Args : none GFF Title : GFF Usage : print $site->GFF(); : print $site->GFF($gff_formatter) Function: returns a "standard" multiline GFF string Returns : a string (multiline, newline terminated) Args : a $gff_formatter function reference (optional) perl v5.14.2 2008-01-24 TFBS::SitePairSet(3pm)

Check Out this Related Man Page

TFBS::Word::Consensus(3pm)				User Contributed Perl Documentation				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 v5.14.2 2008-01-24 TFBS::Word::Consensus(3pm)

Featured Tech Videos