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28 lines
1.3 KiB
Text
28 lines
1.3 KiB
Text
CAPS: Coevolution Analysis using Protein Sequences
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CAPS is aimed at measuring the coevolution between amino acid sites
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belonging to the same protein (intra-molecular coevolution) or to two
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functionally or physically interacting proteins (inter-molecular
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coevolution). The Software implements an improved method to detect
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intra-molecular coevolution as published in Genetics (Fares and Travers,
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2006) and also inter-protein coevolution analysis. The improved scoring
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of amino acid sites is obtained by maximum likelihood ancestral state
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reconstruction along with simulations to assess significance.
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In addition, a test which assesses whether two proteins are interacting
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is implemented.
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NOTE:
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The script just repackages the binaries provided from upstream. If you
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want to compile the program from source check "vCAPS_coevolution", which
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also comes with an unofficial patch that extends the verbosity of the
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results.
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CITING:
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CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
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Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
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The mathematical model has been described separately:
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A novel method for detecting intramolecular coevolution: adding a
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further dimension to selective constraints analyses. Fares MA, Travers
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SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113
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