tfbs::matrix::alignment(3pm) [debian man page]
TFBS::Matrix::Alignment(3pm) User Contributed Perl Documentation TFBS::Matrix::Alignment(3pm) NAME
TFBS::Matrix::Alignment - class for alignment of PFM objects SYNOPSIS
o Making an alignment: (See documentation of individual TFBS::DB::* modules to learn how to connect to different types of pattern databases and retrieve TFBS::Matrix::* objects from them.) my $db_obj = TFBS::DB::JASPAR2->new (-connect => ["dbi:mysql:JASPAR2:myhost", "myusername", "mypassword"]); my $pfm1 = $db_obj->get_Matrix_by_ID("M0001", "PFM"); my $pfm2 = $db_obj->get_Matrix_by_ID("M0002", "PFM"); my $alignment= new TFBS::Matrix::Alignment( -pfm1=>$pfm1, -pfm2=>$pfm2, -binary=>"/TFBS/Ext/matrix_aligner", ); DESCRIPTION
TFBS::Matrix::Alignment is a class for representing and performing pairwise alignments of profiles (in the form of TFBS::PFM objects) Alignments are preformed using a semi-global variant of the Needleman-Wunsch algorithm that only permits the opening of one internal gap. Fore reference, the algorithm is described in Sandelin et al Funct Integr Genomics. 2003 Jun 25 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 $alignment = TFBS::Matrix::Alignment->new(%args) Function: constructor for the TFBS::Matrix::Alignment object Returns : a new TFBS::Matrix::Alignment object Args : # you must specify: -pfm1, # a TFBS::Matrix::PFM object -pfm2, # another TFBS::Matrix::PFM object -binary, # a valid path to the comparison algorithm (matrixalign) ####### -ext_penalty #OPTIONAL gap extension penalty in Needleman-Wunsch algorithmstring. Default 0.01 -open_penalty, #OPTIONAL gap opening penalty in Needleman-Wunsch algorithmstring. Default 3.0 score Title : score Usage : my $score = $alignmentobject->score(); Function: access an alignment score (where each aligned position can contribute max 2) Returns : a floating point number Args : none score Title : gaps Usage : my $nr_of_gaps = $alignmentobject->gaps(); Function: access the number of gaps in an alignment Returns : an integer Args : none length Title : length Usage : my $length = $alignmentobject->length(); Function: access the length of an alignment (ie thenumber of aligned positions) Returns : an integer Args : none strand Title : strand Usage : my $strand = $alignmentobject->strand(); Function: access the oriantation of the aligned patterns: ++= oriented as input +-= second pattern is reverse-complemented Returns : a string Args : none alignment Title : alignment Usage : my $alignment_string = $alignmentobject->alignment(); Function: access a string describing the alignment Returns : an string, where each number refers to a position in repective PFM. Position numbering is according to orientation: ie if the second profile is reversed, position 1 corresponds to the last position in the input profile. Gaps are denoted as - . RXR-VDR - 1 2 3 - 4 5 - PPARgamma-RXRal 1 2 3 4 5 6 7 8 Args : none POD ERRORS
Hey! The above document had some coding errors, which are explained below: Around line 39: You forgot a '=back' before '=head1' perl v5.14.2 2008-01-24 TFBS::Matrix::Alignment(3pm)
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TFBS::Matrix::PWM(3pm) User Contributed Perl Documentation TFBS::Matrix::PWM(3pm) NAME
TFBS::Matrix::PWM - class for position weight matrices of nucleotide patterns SYNOPSIS
o creating a TFBS::Matrix::PWM object manually: my $matrixref = [ [ 0.61, -3.16, 1.83, -3.16, 1.21, -0.06], [-0.15, -2.57, -3.16, -3.16, -2.57, -1.83], [-1.57, 1.85, -2.57, -1.34, -1.57, 1.14], [ 0.31, -3.16, -2.57, 1.76, 0.24, -0.83] ]; my $pwm = TFBS::Matrix::PWM->new(-matrix => $matrixref, -name => "MyProfile", -ID => "M0001" ); # or my $matrixstring = <<ENDMATRIX 0.61 -3.16 1.83 -3.16 1.21 -0.06 -0.15 -2.57 -3.16 -3.16 -2.57 -1.83 -1.57 1.85 -2.57 -1.34 -1.57 1.14 0.31 -3.16 -2.57 1.76 0.24 -0.83 ENDMATRIX ; my $pwm = TFBS::Matrix::PWM->new(-matrixstring => $matrixstring, -name => "MyProfile", -ID => "M0001" ); o retrieving a TFBS::Matix::PWM object from a database: (See documentation of individual TFBS::DB::* modules to learn how to connect to different types of pattern databases and retrieve TFBS::Matrix::* objects from them.) my $db_obj = TFBS::DB::JASPAR2->new (-connect => ["dbi:mysql:JASPAR2:myhost", "myusername", "mypassword"]); my $pwm = $db_obj->get_Matrix_by_ID("M0001", "PWM"); # or my $pwm = $db_obj->get_Matrix_by_name("MyProfile", "PWM"); o retrieving list of individual TFBS::Matrix::PWM objects from a TFBS::MatrixSet object (see decumentation of TFBS::MatrixSet to learn how to create objects for storage and manipulation of multiple matrices) my @pwm_list = $matrixset->all_patterns(-sort_by=>"name"); o scanning a nucleotide sequence with a matrix my $siteset = $pwm->search_seq(-file =>"myseq.fa", -threshold => "80%"); o scanning a pairwise alignment with a matrix my $site_pair_set = $pwm->search_aln(-file =>"myalign.aln", -threshold => "80%", -cutoff => "70%", -window => 50); DESCRIPTION
TFBS::Matrix::PWM is a class whose instances are objects representing position weight matrices (PWMs). A PWM is normally calculated from a raw position frequency matrix (see TFBS::Matrix::PFM for the explanation of position frequency matrices). For example, given the following position frequency matrix: A:[ 12 3 0 0 4 0 ] C:[ 0 0 0 11 7 0 ] G:[ 0 9 12 0 0 0 ] T:[ 0 0 0 1 1 12 ] The standard computational procedure is applied to convert it into the following position weight matrix: A:[ 0.61 -3.16 1.83 -3.16 1.21 -0.06] C:[-0.15 -2.57 -3.16 -3.16 -2.57 -1.83] G:[-1.57 1.85 -2.57 -1.34 -1.57 1.14] T:[ 0.31 -3.16 -2.57 1.76 0.24 -0.83] which contains the "weights" associated with the occurence of each nucleotide at the given position in a pattern. A TFBS::Matrix::PWM object is equipped with methods to search nucleotide sequences and pairwise alignments of nucleotide sequences with the pattern they represent, and return a set of sites in nucleotide sequence (a TFBS::SiteSet object for single sequence search, and a TFBS::SitePairSet for the alignment search). 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 either one of the following three: -matrix, # reference to an array of arrays of integers #or -matrixstring,# a string containing four lines # of tab- or space-delimited integers #or -matrixfile, # the name of a file containing four lines # of tab- or space-delimited integers ####### -name, # string, OPTIONAL -ID, # string, OPTIONAL -class, # string, OPTIONAL -tags # an array 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 -threshold, # minimum score for the hit, either absolute # (e.g. 11.2) or relative (e.g. "75%") # OPTIONAL: default "80%" -subpart # subpart of the sequence to search, given as # -subpart => { start => 140, # end => 180 } # where start and end are coordinates in the # sequence; the coordinate range is interpreted # in the BioPerl tradition (1-based, inclusive) # OPTIONAL: by default searches entire alignment 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 PWM: 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 ############# -threshold, # minimum score for the hit, either absolute # (e.g. 11.2) or relative (e.g. "75%") # OPTIONAL: default "80%" -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%" -subpart # subpart of the alignment to search, given as e.g. # -subpart => { relative_to => 1, # start => 140, # end => 180 } # where start and end are coordinates in the # sequence indicated by relative_to (1 for the # 1st sequence in the alignment, 2 for the 2nd) # OPTIONAL: by default searches entire alignment -conservation # conservation profile, a TFBS::ConservationProfile # OPTIONAL: by default the conservation profile is # computed internally on the fly (less efficient) name ID class matrix length revcom rawprint prettyprint The above methods are common to all matrix objects. Please consult TFBS::Matrix to find out how to use them. perl v5.14.2 2008-01-24 TFBS::Matrix::PWM(3pm)