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Heinz Wiesinger
63daf9f79a
All: Support $PRINT_PACKAGE_NAME env var
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| CAPS_coevolution.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 3 éve |
| CAPS_coevolution.info | 80d665841b academic/CAPS_coevolution: Added (Coevolution Analysis). | 7 éve |
| README | e14ced8086 academic/CAPS_coevolution: update Copyright years and README | 3 éve |
| References | 80d665841b academic/CAPS_coevolution: Added (Coevolution Analysis). | 7 éve |
| slack-desc | 80d665841b academic/CAPS_coevolution: Added (Coevolution Analysis). | 7 éve |
README
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. If you
want to compile the program from source check "vCAPS_coevolution", which
also comes with an unofficial patch that extends the verbosity of the
results.
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
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. If you
want to compile the program from source check "vCAPS_coevolution", which
also comes with an unofficial patch that extends the verbosity of the
results.
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