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TFBS::Matrix::Alignment.3pm

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'