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 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

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 39:
           You forgot a '=back' before '=head1'