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)