NAME¶
TFBS::Matrix::Alignment - class for alignment of PFM objects
SYNOPSIS¶
- •
- 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'