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 NeedlemanWunsch 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 v5.10.1 2008-01-24 TFBS::Matrix::Alignment(3pm)