NAME

Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.

SYNOPSIS

use Bio::Matrix::PSM::ProtMatrix;
# Create from memory by supplying probability matrix hash both as strings or
# arrays where the frequencies   Hash entries of the form lN refer to an array
# of position-specific log-odds scores for amino acid N. Hash entries of the
# form pN represent the position-specific probability of finding amino acid N.

my %param = (
          'id' => 'A. thaliana protein atp1',
          '-e_val' => $score,
          'lS' => [ '-2', '3', '-3', '2', '-3', '1', '1', '3' ],
          'lF' => [ '-1', '-4', '0', '-5', '0', '-5', '-4', '-4' ],
          'lT' => [ '-1', '1', '0', '1', '-2', '-1', '0', '1' ],
          'lN' => [ '-3', '-1', '-2', '3', '-5', '5', '-2', '0' ],
          'lK' => [ '-2', '0', '-3', '2', '-3', '2', '-3', '-1' ],
          'lY' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-4', '-4' ],
          'lE' => [ '-3', '4', '-3', '2', '-4', '-2', '-3', '2' ],
          'lV' => [ '0', '-2', '1', '-4', '1', '-4', '-1', '-3' ],
          'lQ' => [ '-1', '0', '-2', '3', '-4', '1', '-3', '0' ],
          'lM' => [ '8', '-3', '8', '-3', '1', '-3', '-3', '-3' ],
          'lC' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-3', '-3' ],
          'lL' => [ '1', '-3', '1', '-4', '3', '-4', '-2', '-4' ],
          'lA' => [ '-2', '1', '-2', '0', '-2', '-2', '2', '2' ],
          'lW' => [ '-2', '-4', '-3', '-5', '-4', '-5', '-5', '-5' ],
          'lP' => [ '-3', '-2', '-4', '-3', '-1', '-3', '6', '-3' ],
          'lH' => [ '-2', '-2', '-3', '-2', '-5', '-2', '-2', '-3' ],
          'lD' => [ '-4', '-1', '-3', '1', '-3', '-1', '-3', '4' ],
          'lR' => [ '-2', '-1', '-3', '0', '-4', '4', '-4', '-3' ],
          'lI' => [ '0', '-3', '0', '-4', '6', '-4', '-2', '-2' ],
          'lG' => [ '-4', '-2', '-4', '-2', '-5', '-3', '-1', '-2' ],
          'pS' => [ '0', '33', '0', '16', '1', '12', '11', '25' ],
          'pF' => [ '0', '0', '2', '0', '3', '0', '0', '0' ],
          'pT' => [ '0', '8', '7', '10', '1', '2', '7', '8' ],
          'pN' => [ '0', '0', '2', '13', '0', '36', '1', '4' ],
          'pK' => [ '0', '5', '0', '13', '1', '15', '0', '2' ],
          'pY' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
          'pE' => [ '0', '41', '1', '12', '0', '0', '0', '15' ],
          'pV' => [ '0', '3', '9', '0', '2', '0', '3', '1' ],
          'pQ' => [ '0', '0', '0', '15', '0', '4', '0', '3' ],
          'pM' => [ '100', '0', '66', '0', '2', '0', '0', '0' ],
          'pC' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
          'pL' => [ '0', '0', '8', '0', '25', '0', '4', '0' ],
          'pA' => [ '0', '10', '1', '9', '2', '0', '22', '16' ],
          'pW' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
          'pP' => [ '0', '0', '0', '0', '3', '1', '45', '0' ],
          'pH' => [ '0', '0', '0', '0', '0', '0', '1', '0' ],
          'pD' => [ '0', '0', '1', '7', '2', '2', '0', '22' ],
          'pR' => [ '0', '0', '0', '3', '0', '27', '0', '0' ],
          'pI' => [ '0', '0', '3', '0', '59', '1', '2', '3' ],
          'pG' => [ '0', '0', '0', '1', '0', '0', '4', '1' ],
);

my $matrix = Bio::Matrix::PSM::ProtMatrix( %param );


my $site = Bio::Matrix::PSM::ProtMatrix->new(%param);
# Or get it from a file:
use Bio::Matrix::PSM::IO;
my $psmIO = Bio::Matrix::PSM::IO->new(-file => $file, -format => 'psi-blast');
while (my $psm = $psmIO->next_psm) {
   #Now we have a Bio::Matrix::PSM::Psm object, 
   # see Bio::Matrix::PSM::PsmI for details
   #This is a Bio::Matrix::PSM::ProtMatrix object now
   my $matrix = $psm->matrix;   
}

# Get a simple consensus, where alphabet is:
# {A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V,}
# choosing the highest probability or N if prob is too low
my $consensus = $site->consensus;

# Retrieving and using regular expressions:
my $regexp = $site->regexp;
my $count = grep($regexp,$seq);
my $count = ($seq=~ s/$regexp/$1/eg);
print "Motif $mid is present $count times in this sequence\n";

DESCRIPTION

ProtMatrix is designed to provide some basic methods when working with position scoring (weight) matrices related to protein sequences. A protein PSM consists of 20 vectors with 20 frequencies (one per amino acid per position). This is the minimum information you should provide to construct a PSM object. The vectors can be provided as strings with frequencies where the frequency is {0..a} and a=1. This is the way MEME compressed representation of a matrix and it is quite useful when working with relational DB. If arrays are provided as an input (references to arrays actually) they can be any number, real or integer (frequency or count).

When creating the object the constructor will check for positions that equal 0. If such is found it will increase the count for all positions by one and recalculate the frequency. Potential bug - if you are using frequencies and one of the positions is 0 it will change significantly. However, you should never have frequency that equals 0.

Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest.

Summary of the methods I use most frequently (details below):

iupac - return IUPAC compliant consensus as a string
score - Returns the score as a real number
IC - information content. Returns a real number
id - identifier. Returns a string
accession - accession number. Returns a string
next_pos - return the sequence probably for each letter, IUPAC
      symbol, IUPAC probability and simple sequence
consenus letter for this position. Rewind at the end. Returns a hash.
pos - current position get/set. Returns an integer.
regexp - construct a regular expression based on IUPAC consensus.
      For example AGWV will be [Aa][Gg][AaTt][AaCcGg]
width - site width
get_string - gets the probability vector for a single base as a string.
get_array - gets the probability vector for a single base as an array.
get_logs_array - gets the log-odds vector for a single base as an array.

New methods, which might be of interest to anyone who wants to store PSM in a relational database without creating an entry for each position is the ability to compress the PSM vector into a string with losing usually less than 1% of the data. this can be done with:

my $str=$matrix->get_compressed_freq('A');
or

my $str=$matrix->get_compressed_logs('A');

Loading from a database should be done with new, but is not yet implemented. However you can still uncompress such string with:

my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1,1); for PSM

or

my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1000,2); for log odds

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - James Thompson

Email tex@biosysadmin.com

APPENDIX

new

Title    : new
Usage    : my $site = Bio::Matrix::PSM::ProtMatrix->new( 
              %probs,
              %logs,
              -IC    => $ic,
              -e_val => $score, 
              -id    => $mid
              -model => \%model
           );
Function : Creates a new Bio::Matrix::PSM::ProtMatrix object from memory
Throws   : If inconsistent data for all vectors (all 20 amino acids) is
              provided, if you mix input types (string vs array) or if a
              position freq is 0.
Example  :
Returns  : Bio::Matrix::PSM::ProtMatrix object
Args     : Hash references to log-odds scores and probabilities for
           position-specific scoring info, e-value (optional), information
           content (optional), id (optional), model for background distribution
           of proteins (optional).

alphabet

Title    : Returns an array (or array reference if desired) to the alphabet 
Usage    :
Function : Returns an array (or array reference) containing all of the
           allowable characters for this matrix.
Throws   :
Example  :
Returns  : Array or arrary reference.
Args     :

_calculate_consensus

Title    : _calculate_consensus
Usage    :
Function : Calculates the consensus sequence for this matrix. 
Throws   :
Example  :
Returns  :
Args     :

next_pos

Title    : next_pos
Usage    :
Function : Retrieves the next position features: frequencies for all 20 amino
           acids, log-odds scores for all 20 amino acids at this position,
           the main (consensus) letter at this position, the probability
           for the consensus letter to occur at this position and the relative
           current position as an integer.
Throws   :
Example  :
Returns  : hash (or hash reference) (pA,pR,pN,pD,...,logA,logR,logN,logD,aa,prob,rel)
           - pN entries represent the probability for amino acid N
           to be at this position
           - logN entries represent the log-odds score for having amino acid
           N at this position
           - aa is the consensus amino acid
           - prob is the probability for the consensus amino acid to be at this 
           position
           - rel is the relative index of the current position (integer)
Args      : none

curpos

Title    : curpos
Usage    :
Function : Gets/sets the current position. 
Throws   :
Example  :
Returns  : Current position (integer).
Args     : New position (integer).

e_val

Title    : e_val
Usage    :
Function : Gets/sets the e-value
Throws   :
Example  :
Returns  : 
Args     : real number

IC

Title    : IC
Usage    :
Function : Position-specific information content.
Throws   :
Example  :
Returns  : Information content for current position.
Args     : Information content for current position.

accession_number

Title    : accession_number
Usage    :
Function: accession number, this will be unique id for the ProtMatrix object as
           well for any other object, inheriting from ProtMatrix.
Throws   :
Example  :
Returns  : New accession number (string)
Args     : Accession number (string)

consensus

Title    : consensus
Usage    :
Function : Returns the consensus sequence for this PSM.
Throws   : if supplied with thresold outisde 5..10 range
Example  :
Returns  : string
Args     : (optional) threshold value 5 to 10 (corresponds to 50-100% at each position

get_string

Title   : get_string
Usage   :
Function: Returns given probability vector as a string. Useful if you want to
           store things in a rel database, where arrays are not first choice
Throws  : If the argument is outside {A,C,G,T}
Example :
Returns : string
Args    : character {A,C,G,T}

width

Title    : width
Usage    :
Function : Returns the length of the site
Throws   :
Example  :
Returns  : number
Args     :

get_array

Title    : get_array
Usage    :
Function : Returns an array with frequencies for a specified amino acid.
Throws   :
Example  :
Returns  : Array representing frequencies for specified amino acid.
Args     : Single amino acid (character).

get_logs_array

Title    : get_logs_array
Usage    :
Function : Returns an array with log_odds for a specified base
Throws   :
Example  :
Returns  : Array representing log-odds scores for specified amino acid.
Args     : Single amino acid (character).

id

Title    : id
Usage    :
Function : Gets/sets the site id
Throws   :
Example  :
Returns  : string
Args     : string

regexp

Title    : regexp
Usage    :
Function : Returns a case-insensitive regular expression which matches the
           IUPAC convention.  X's in consensus sequence will match anything.     
Throws   :
Example  :
Returns  : string
Args     : Threshold for calculating consensus sequence (number in range 0-100
           representing a percentage). Threshold defaults to 20.

regexp_array

Title    : regexp_array
Usage    :
Function : Returns an array of position-specific regular expressions.
            X's in consensus sequence will match anything.      
Throws   :
Example  :
Returns  : Array of position-specific regular expressions.
Args     : Threshold for calculating consensus sequence (number in range 0-100
           representing a percentage). Threshold defaults to 20.
Notes    : Simply calls regexp method in list context.

_compress_array

Title    : _compress_array
Usage    :
Function :  Will compress an array of real signed numbers to a string (ie vector of bytes)
            -127 to +127 for bi-directional(signed) and 0..255 for unsigned ;
Throws   :
Example  :  Internal stuff
Returns  :  String
Args     :  array reference, followed by max value and direction (optional, defaults to 1),
            direction of 1 is unsigned, anything else is signed. 

_uncompress_string

Title    : _uncompress_string
Usage    :
Function :   Will uncompress a string (vector of bytes) to create an array of real
                 signed numbers (opposite to_compress_array)
Throws   :
Example  :   Internal stuff
Returns  :   string, followed by max value and direction (optional, defaults to 1),
             direction of 1 is unsigned, anything else is signed.
Args     :   array

get_compressed_freq

Title    : get_compressed_freq
Usage    :
Function:   A method to provide a compressed frequency vector. It uses one byte to
            code the frequence for one of the probability vectors for one position.
            Useful for relational database. Improvement of the previous 0..a coding.
Throws   :
Example  :   my $strA=$self->get_compressed_freq('A');
Returns  :   String
Args     :   char 

sequence_match_weight

Title    : sequence_match_weight
Usage    :
Function :   This method will calculate the score of a match, based on the PSM
             if such is associated with the matrix object. Returns undef if no
             PSM data is available.
Throws   :   if the length of the sequence is different from the matrix width
Example  :   my $score=$matrix->sequence_match_weight('ACGGATAG');
Returns  :   Floating point
Args     :   string

_to_IUPAC

Title   : _to_IUPAC
Usage   :
Function: Converts a single position to IUPAC compliant symbol and returns its probability.
           Currently returns the most likely amino acid/probability combination.
Throws  :
Example :
Returns : char, real number representing an amino acid and a probability.
Args    : real numbers for all 20 amino acids (ordered by alphabet contained
           in $self->{_alphabet}, minimum probability threshold.

_to_cons

Title   : _to_cons
Usage   :
Function: Converts a single position to simple consensus character and returns
           its probability. Currently just calls the _to_IUPAC subroutine. 
Throws  :
Example :
Returns : char, real number
Args    : real numbers for A,C,G,T (positional)

get_all_vectors

Title    : get_all_vectors
Usage    :
Function :  returns all possible sequence vectors to satisfy the PFM under
            a given threshold
Throws   :  If threshold outside of 0..1 (no sense to do that)
Example  :  my @vectors = $self->get_all_vectors(4);
Returns  :  Array of strings
Args     :  (optional) floating

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq