Provided by: libtfbs-perl_0.7.1-2_amd64
TFBS::Matrix::Alignment - class for alignment of PFM objects
· 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", );
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
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AUTHOR - Boris Lenhard
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
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 respective 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
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