About

This server provides an online interface to CAPS version 2, a Perl program that performs Coevolution Analysis using Protein Sequences, i.e. it searches through a set of homologous sequences and detects groups of amino acids that evolve together. The results can indicate functionally or structurally linked regions that are subjected to strong selective constraints. An older version is available here.

This website is free and open to all users and there is no login requirement.

Note: This version is still under development and results are not comparable to the original CAPS version.

News

- Mon 26 May 2014
CAPS version 2 is replacing the original version and features the following improvements:

• improved scoring of amino acid sites
• 10-fold speed-up
• automatic detection of PDB structure
• more powerful server
• better queueing system

→ try it now!

Citation

If you use CAPS in your research, please include the following citation:

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

Acknowledgements

Funding and support from the following resources allowed this project to be realised:

	Science Foundation Ireland Principal Investigator Award
	Trinity College Dublin, Ireland
	Smurfit Institute of Genetics