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)