README 1.3 KB

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  1. CAPS: Coevolution Analysis using Protein Sequences
  2. CAPS is aimed at measuring the coevolution between amino acid sites
  3. belonging to the same protein (intra-molecular coevolution) or to two
  4. functionally or physically interacting proteins (inter-molecular
  5. coevolution). The Software implements an improved method to detect
  6. intra-molecular coevolution as published in Genetics (Fares and Travers,
  7. 2006) and also inter-protein coevolution analysis. The improved scoring
  8. of amino acid sites is obtained by maximum likelihood ancestral state
  9. reconstruction along with simulations to assess significance.
  10. In addition, a test which assesses whether two proteins are interacting
  11. is implemented.
  12. NOTE:
  13. The script just repackages the binaries provided from upstream. If you
  14. want to compile the program from source check "vCAPS_coevolution", which
  15. also comes with an unofficial patch that extends the verbosity of the
  16. results.
  17. CITING:
  18. CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
  19. Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
  20. The mathematical model has been described separately:
  21. A novel method for detecting intramolecular coevolution: adding a
  22. further dimension to selective constraints analyses. Fares MA, Travers
  23. SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113