DEBIAN/SCORE_CONSERVATION(1) | User Commands | DEBIAN/SCORE_CONSERVATION(1) |
score_conservation - score protein sequence conservation
score_conservation [options] ALIGNFILE
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.
Equation:
"score = (1 - lambda) * average_score_over_window_around_middle + lambda * score_of_middle"
Some methods, e.g. js_divergence, do not use this.
Note: you may have to copy and uncompress the example data files before running the following examples.
score_conservation /usr/share/doc/conservation-code/examples/2plc__hssp-filtered.aln
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
2018-10-15 | 20110309.0 |