Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object


         $dis = Bio::SearchDist->new();
         foreach $score ( @scores ) {

         if( $dis->fit_evd() ) {
           foreach $score ( @scores ) {
             $evalue = $dis->evalue($score);
             print "Score $score had an evalue of $evalue\n";
         } else {
           warn("Could not fit histogram to an EVD!");


       The Bio::SearchDist object is a wrapper around Sean Eddy's excellent histogram object. The
       histogram object can bascially take in a number of scores which are sensibly distributed
       somewhere around 0 that come from a supposed Extreme Value Distribution. Having add all
       the scores from a database search via the add_score method you can then fit a extreme
       value distribution using fit_evd(). Once fitted you can then get out the evalue for each
       score (or a new score) using evalue($score).

       The fitting procedure is better described in Sean Eddy's own code (available from, or in the histogram.h header file in Compile/SW). Bascially it
       fits a EVD via a maximum likelhood method with pruning of the top end of the distribution
       so that real positives are discarded in the fitting procedure. This comes from an
       originally idea of Richard Mott's and the likelhood fitting is from a book by Lawless
       [should ref here].

       The object relies on the fact that the scores are sensibly distributed around about 0 and
       that integer bins are sensible for the histogram. Scores based on bits are often ideal for
       this (bits based scoring mechanisms is what this histogram object was originally designed


       The original code this was based on comes from the histogram module as part of the HMMer2
       package. Look at

       Its use in Bioperl is via the Compiled XS extension which is cared for by Ewan Birney
       ( Please contact Ewan first about the use of this module


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       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : add_score
        Usage   : $dis->add_score(300);
        Function: Adds a single score to the distribution
        Returns : nothing
        Args    :

        Title   : fit_evd
        Usage   : $dis->fit_evd();
        Function: fits an evd to the current distribution
        Returns : 1 if it fits successfully, 0 if not
        Args    :

        Title   : fit_Gaussian
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : evalue
        Usage   : $eval = $dis->evalue($score)
        Function: Returns the evalue of this score
        Returns : float
        Args    :

        Title   : _engine
        Usage   : $obj->_engine($newval)
        Function: underlyine bp_sw:: histogram engine
        Returns : value of _engine
        Args    : newvalue (optional)