NAME

       score_conservation - score protein sequence conservation

SYNOPSIS

       score_conservation [options] ALIGNFILE

DESCRIPTION

       Score protein sequence conservation in ALIGNFILE.  ALIGNFILE must be in FASTA, CLUSTAL or
       Stockholm format.

       The following conservation scoring methods are implemented:
        * sum of pairs
        * weighted sum of pairs
        * Shannon entropy
        * Shannon entropy with property groupings (Mirny and Shakhnovich 1995,
          Valdar and Thornton 2001)
        * relative entropy with property groupings (Williamson 1995)
        * von Neumann entropy (Caffrey et al 2004)
        * relative entropy (Samudrala and Wang 2006)
        * Jensen-Shannon divergence (Capra and Singh 2007)

       A window-based extension that incorporates the estimated conservation of sequentially
       adjacent residues into the score for each column is also given.  This window approach can
       be applied to any of the conservation scoring methods.

       With default parameters score_conservation(1) computes the conservation scores for the
       alignment using the Jensen-Shannon divergence and a window -w of 3.

       The sequence-specific output can be used as the conservation input for concavity(1).

       Conservation is highly predictive in identifying catalytic sites and residues near bound
       ligands.

REFERENCES

       Capra JA and Singh M. Predicting functionally important residues from sequence
       conservation. Bioinformatics, 23(15):1875-82, 2007.

OPTIONS

       -a [NAME]
           Reference sequence. Print scores in reference to the named sequence (ignoring gaps).
           Default prints the entire column.

       -b [0-1]
           Lambda for window heuristic linear combination. Default=.5.

           Equation:

           "score = (1 - lambda) * average_score_over_window_around_middle + lambda *
           score_of_middle"

       -d [FILE]
           Background distribution file, e.g. distributions/swissprot.distribution.
           Default=built-in BLOSUM62.

       -g [0-1)]
           Gap cutoff. Do not score columns that contain more than gap cutoff fraction gaps.
           Default=.3.

       -h  Print help.

       -l [true|false]
           Use sequence weighting. Default=true.

       -m [FILE]
           Similarity matrix file, e.g. matrix/blosum62.bla or .qij. Default=matrix/blosum62.bla.

           Some methods, e.g. js_divergence, do not use this.

       -n [true|false]
           Normalize scores. Print the z-score (over the alignment) of each column raw score.
           Default=false.

       -o FILE
           Output file. Default: standard output stream.

       -p [true|false]
           Use gap penalty. Lower the score of columns that contain gaps, proportionally to the
           sum weight of the gapped sequences. Default=true.

       -s [METHOD]
           Conservation estimation method, one of shannon_entropy property_entropy
           property_relative_entropy vn_entropy relative_entropy js_divergence sum_of_pairs.
           Default=js_divergence.

       -w [0-INT]
           Window size. Number of residues on either side included in the window. Default=3.

EXAMPLES

       Note: you may have to copy and uncompress the example data files before running the
       following examples.

       Compute conservation scores for the alignment using the Jensen-Shannon divergence with
       default settings and print out the scores:
            score_conservation /usr/share/doc/conservation-code/examples/2plc__hssp-filtered.aln

       Score an alignment using Jensen-Shannon divergence, a window of size 3 (on either side of
       the residue), and the swissprot background distribution:
            score_conservation -s js_divergence -w 3 -d \
             /usr/share/conservation-code/distributions/swissprot.distribution \
             /usr/share/doc/conservation-code/examples/2plc__hssp-filtered.aln

FILES

       Distributions
           /usr/share/conservation-code/distributions

       Matrices
           /usr/share/conservation-code/matrix

SEE ALSO

       Homepage <http://compbio.cs.princeton.edu/conservation/>
       Publication <http://bioinformatics.oxfordjournals.org/cgi/content/full/23/15/1875>
       concavity(1)