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authorPetar Petrov <slackalaxy@gmail.com>2017-02-04 16:40:59 +0000
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2017-02-11 07:24:07 +0700
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tree9fe086d0dcee30f9986daf1d9ca4ec49b1eebf3d /academic/CAPS_coevolution/README
parent1852c5a4c13f778f2958fdb83945ce7e068196b8 (diff)
academic/CAPS_coevolution: Added (Coevolution Analysis).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
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+CAPS: Coevolution Analysis using Protein Sequences
+
+CAPS is aimed at measuring the coevolution between amino acid sites
+belonging to the same protein (intra-molecular coevolution) or to two
+functionally or physically interacting proteins (inter-molecular
+coevolution). The Software implements an improved method to detect
+intra-molecular coevolution as published in Genetics (Fares and Travers,
+2006) and also inter-protein coevolution analysis. The improved scoring
+of amino acid sites is obtained by maximum likelihood ancestral state
+reconstruction along with simulations to assess significance.
+
+In addition, a test which assesses whether two proteins are interacting
+is implemented.
+
+NOTE:
+The script just repackages the binaries provided from upstream.
+
+CITING:
+CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
+Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
+
+The mathematical model has been described separately:
+A novel method for detecting intramolecular coevolution: adding a
+further dimension to selective constraints analyses. Fares MA, Travers
+SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113