Bio::Matrix::PSM::SiteMatrixI - SiteMatrix interface, holds a position scoring matrix (or position weight matrix) use Bio::Matrix::PSM::SiteMatrix; # Create from memory by supplying probability matrix hash # both as strings or arrays my ($a,$c,$g,$t,$score,$ic, $mid)=@_; # where $a,$c,$g and $t are either arrayref or string # or my ($a,$c,$g,$t,$score,$ic,$mid)= ('05a011','110550','400001','100104',0.001,19.2,'CRE1'); # Where a stands for all (this frequency=1), see explanation bellow my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t,-IC=>$ic, -e_val=>$score, -id=>$mid); my $site=new Bio::Matrix::PSM::SiteMatrix(%param); # Or get it from a file: use Bio::Matrix::PSM::IO; my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'transfac'); while (my $psm=$psmIO->next_psm) { # Now we have a Bio::Matrix::PSM::Psm object, see # Bio::Matrix::PSM::PsmI for details my $matrix=$psm->matrix; # This is a Bio::Matrix::PSM::SiteMatrix object now } # Get a simple consensus, where alphabet is {A,C,G,T,N}, choosing # the highest probability or N if prob is too low my $consensus=$site->consensus; #Getting/using regular expression 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"; SiteMatrix is designed to provide some basic methods when working with position scoring (weight) matrices, such as transcription factor binding sites for example. A DNA PSM consists of four vectors with frequencies {A,C,G,T). 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 bellow): 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.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email skirov@utk.edu

new
Title : new Usage : my $site=new Bio::Matrix::PSM::SiteMatrix (-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t, -IC=>$ic,-e_val=>$score, -id=>$mid); Function: Creates a new Bio::Matrix::PSM::SiteMatrix object from memory Throws : If inconsistent data for all vectors (A,C,G and T) is provided, if you mix input types (string vs array) or if a position freq is 0. Example : Returns : Bio::Matrix::PSM::SiteMatrix object Args : hash

next_pos
Title : next_pos Usage : my %base=$site->next_pos; Function: Retrieves the next position features: frequencies for A,C,G,T, the main letter (as in consensus) and the probabilty for this letter to occur at this position and the current position Throws : Example : Returns : hash (pA,pC,pG,pT,base,prob,rel) Args : none

curpos
Title : curpos Usage : my $pos=$site->curpos; Function: Gets/sets the current position. Converts to 0 if argument is minus and to width if greater than width Throws : Example : Returns : integer Args : integer

e_val
Title : e_val Usage : my $score=$site->e_val; Function: Gets/sets the e-value Throws : Example : Returns : real number Args : real number

consensus
Title : consensus Usage : my $consensus=$site->consensus; Function: Returns the consensus Throws : Example : Returns : string Args :

accession_number
Title : accession_number Usage : Function: accession number, this will be unique id for the SiteMatrix object as well for any other object, inheriting from SiteMatrix Throws : Example : Returns : string Args : string

width
Title : width Usage : my $width=$site->width; Function: Returns the length of the site Throws : Example : Returns : number Args :

IUPAC
Title : IUPAC Usage : my $iupac_consensus=$site->IUPAC; Function: Returns IUPAC compliant consensus Throws : Example : Returns : string Args :

IC
Title : IC Usage : my $ic=$site->IC; Function: Information content Throws : Example : Returns : real number Args : none

get_string
Title : get_string Usage : my $freq_A=$site->get_string('A'); 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}

id
Title : id Usage : my $id=$site->id; Function: Gets/sets the site id Throws : Example : Returns : string Args : string

regexp
Title : regexp Usage : my $regexp=$site->regexp; Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Throws : Example : Returns : string Args :

regexp_array
Title : regexp_array Usage : my @regexp=$site->regexp; Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Throws : Example : Returns : array Args : To do : I have separated regexp and regexp_array, but maybe they can be rewritten as one - just check what should be returned

get_array
Title : get_array Usage : my @freq_A=$site->get_array('A'); Function: Returns an array with frequencies for a specified base Throws : Example : Returns : array Args : char

_to_IUPAC
Title : _to_IUPAC Usage : Function: Converts a single position to IUPAC compliant symbol and returns its probability. For rules see the implementation. Throws : Example : Returns : char, real number Args : real numbers for A,C,G,T (positional)

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

_calculate_consensus
Title : _calculate_consensus Usage : Function: Internal stuff Throws : Example : Returns : Args :