COMA

COMA: a method for detection of distant evolutionary relationships

Access the COMA web server here.

COMA (Comparison Of Multiple Alignments) is a method for detection of distant evolutionary relationship (homology) through comparison of multiple protein sequence alignments. For convenience, the COMA software package includes programs for constructing profiles from multiple alignments, generating a profile database from a set of profiles, searching a profile (multiple alignment) against a profile database, etc. COMA output consists of pairwise alignments between profiles (multiple alignments) with estimated values of statistical significance, which indicates the probability that the aligned pair of profiles is a random match.

The COMA installation package includes binaries for Linux x86, Linux x86_64, and MS Win32 platforms. The package includes source files as well, so you are free to build the programs on any other system. The instructions in the README file will provide a guidance how to do it.

The COMA software package is licensed under a Creative Commons Attribution-Noncommercial 3.0 Unported License.

To install COMA, download the most recent version:
coma.1.10.tgz [version 1.10] [~31M]

Previous versions:
coma.1.05.tgz [version 1.05] [~30M]
coma.1.02.tgz [version 1.02] [~30M]
coma.0.41.tgz [version 0.41] [~28M]

Uncompress the archive (tar -zxf <filename.tgz>) and follow the instructions in the README file.

Data files

In the Data Files directory, you will find regularly updated archived COMA profile databases (the same ones as used by the COMA server) for PDB filtered at 40% sequence identity, SCOP filtered at 40% sequence identity, and PFAM. The profile databases are in the text format and are cross-platform portable.

Reference:

Margelevičius M., Venclovas Č. (2010) Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparisons. BMC Bioinformatics, 11:89.