Reference

TFBS::Matrix::PWM(3pm)

class for position weight matrices of nucleotide patterns

NAME

TFBS::Matrix::PWM - class for position weight matrices of nucleotide patterns

SYNOPSIS

•

creating a TFBS::Matrix::PWM object manually:

    my $matrixref = [ [ 0.61, -3.16,  1.83, -3.16,  1.21, -0.06],
                      [-0.15, -2.57, -3.16, -3.16, -2.57, -1.83],
                      [-1.57,  1.85, -2.57, -1.34, -1.57,  1.14],
                      [ 0.31, -3.16, -2.57,  1.76,  0.24, -0.83]
                    ];
    my $pwm = TFBS::Matrix::PWM->new(-matrix => $matrixref,
                                     -name   => "MyProfile",
                                     -ID     => "M0001"
                                    );
    # or
    my $matrixstring = <<ENDMATRIX
     0.61 -3.16  1.83 -3.16  1.21 -0.06
    -0.15 -2.57 -3.16 -3.16 -2.57 -1.83
    -1.57  1.85 -2.57 -1.34 -1.57  1.14
     0.31 -3.16 -2.57  1.76  0.24 -0.83
    ENDMATRIX
    ;
    my $pwm = TFBS::Matrix::PWM->new(-matrixstring => $matrixstring,
                                     -name         => "MyProfile",
                                     -ID           => "M0001"
                                    );
•

retrieving a TFBS::Matix::PWM object from a database:

(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 $pwm = $db_obj->get_Matrix_by_ID("M0001", "PWM");
    # or
    my $pwm = $db_obj->get_Matrix_by_name("MyProfile", "PWM");
•

retrieving list of individual TFBS::Matrix::PWM objects from a TFBS::MatrixSet object

(see decumentation of TFBS::MatrixSet to learn how to create objects for storage and manipulation of multiple matrices)

    my @pwm_list = $matrixset->all_patterns(-sort_by=>"name");
•

scanning a nucleotide sequence with a matrix

    my $siteset = $pwm->search_seq(-file      =>"myseq.fa",
                                   -threshold => "80%");
•

scanning a pairwise alignment with a matrix

    my $site_pair_set = $pwm->search_aln(-file      =>"myalign.aln",
                                         -threshold => "80%",
                                         -cutoff    => "70%",
                                         -window    => 50);

DESCRIPTION

TFBS::Matrix::PWM is a class whose instances are objects representing position weight matrices (PWMs). A PWM is normally calculated from a raw position frequency matrix (see TFBS::Matrix::PFM for the explanation of position frequency matrices). For example, given the following position frequency matrix:

    A:[ 12     3     0     0     4     0  ]
    C:[  0     0     0    11     7     0  ]
    G:[  0     9    12     0     0     0  ]
    T:[  0     0     0     1     1    12  ]

The standard computational procedure is applied to convert it into the following position weight matrix:

    A:[ 0.61 -3.16  1.83 -3.16  1.21 -0.06]
    C:[-0.15 -2.57 -3.16 -3.16 -2.57 -1.83]
    G:[-1.57  1.85 -2.57 -1.34 -1.57  1.14]
    T:[ 0.31 -3.16 -2.57  1.76  0.24 -0.83]

which contains the "weights" associated with the occurrence of each nucleotide at the given position in a pattern.

A TFBS::Matrix::PWM object is equipped with methods to search nucleotide sequences and pairwise alignments of nucleotide sequences with the pattern they represent, and return a set of sites in nucleotide sequence (a TFBS::SiteSet object for single sequence search, and a TFBS::SitePairSet for the alignment search).

FEEDBACK

Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

Boris Lenhard <[email protected]>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.

new

 Title   : new
 Usage   : my $pwm = TFBS::Matrix::PWM->new(%args)
 Function: constructor for the TFBS::Matrix::PWM object
 Returns : a new TFBS::Matrix::PWM object
 Args    : # you must specify either one of the following three:
           -matrix,      # reference to an array of arrays of integers
              #or
           -matrixstring,# a string containing four lines
                         # of tab- or space-delimited integers
              #or
           -matrixfile,  # the name of a file containing four lines
                         # of tab- or space-delimited integers
           #######
           -name,        # string, OPTIONAL
           -ID,          # string, OPTIONAL
           -class,       # string, OPTIONAL
           -tags         # an array reference, OPTIONAL

search_seq

 Title   : search_seq
 Usage   : my $siteset = $pwm->search_seq(%args)
 Function: scans a nucleotide sequence with the pattern represented
           by the PWM
 Returns : a TFBS::SiteSet object
 Args    : # you must specify either one of the following three:
           -file,       # the name od a fasta file (single sequence)
              #or
           -seqobj      # a Bio::Seq object
                        # (more accurately, a Bio::PrimarySeqobject or a
                        #  subclass thereof)
              #or
           -seqstring # a string containing the sequence
           -threshold,  # minimum score for the hit, either absolute
                        # (e.g. 11.2) or relative (e.g. "75%")
                        # OPTIONAL: default "80%"
           -subpart     # subpart of the sequence to search, given as
                        # -subpart => { start => 140,
                        #               end   => 180 }
                        # where start and end are coordinates in the
                        # sequence; the coordinate range is interpreted
                        # in the BioPerl tradition (1-based, inclusive)
                        # OPTIONAL: by default searches entire alignment

search_aln

 Title   : search_aln
 Usage   : my $site_pair_set = $pwm->search_aln(%args)
 Function: Scans a pairwise alignment of nucleotide sequences
           with the pattern represented by the PWM: it reports only
           those hits that are present in equivalent positions of both
           sequences and exceed a specified threshold score in both, AND
           are found in regions of the alignment above the specified
           conservation cutoff value.
 Returns : a TFBS::SitePairSet object
 Args    : # you must specify either one of the following three:
           -file,       # the name of the alignment file in Clustal
                               format
              #or
           -alignobj      # a Bio::SimpleAlign object
                        # (more accurately, a Bio::PrimarySeqobject or a
                        #  subclass thereof)
              #or
           -alignstring # a multi-line string containing the alignment
                        # in clustal format
           #############
           -threshold,  # minimum score for the hit, either absolute
                        # (e.g. 11.2) or relative (e.g. "75%")
                        # OPTIONAL: default "80%"
           -window,     # size of the sliding window (inn nucleotides)
                        # for calculating local conservation in the
                        # alignment
                        # OPTIONAL: default 50
           -cutoff      # conservation cutoff (%) for including the
                        # region in the results of the pattern search
                        # OPTIONAL: default "70%"
           -subpart     # subpart of the alignment to search, given as e.g.
                        # -subpart => { relative_to => 1,
                        #               start       => 140,
                        #               end         => 180 }
                        # where start and end are coordinates in the
                        # sequence indicated by relative_to (1 for the
                        # 1st sequence in the alignment, 2 for the 2nd)
                        # OPTIONAL: by default searches entire alignment
           -conservation
                        # conservation profile, a TFBS::ConservationProfile
                        # OPTIONAL: by default the conservation profile is
                        # computed internally on the fly (less efficient)

name

ID

class

matrix

length

revcom

rawprint

prettyprint

The above methods are common to all matrix objects. Please consult TFBS::Matrix to find out how to use them.

History