Efficient methods for estimating amino acid replacement rates
2006 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 62, no 6, 663-673 p.Article in journal (Refereed) Published
Replacement rate matrices describe the process of evolution at one position in a protein and are used in many applications where proteins are studied with an evolutionary perspective. Several general matrices have been suggested and have proved to be good approximations of the real process. However, there are data for which general matrices are inappropriate, for example, special protein families, certain lineages in the tree of life, or particular parts of proteins. Analysis of such data could benefit from adaption of a data-specific rate matrix. This paper suggests two new methods for estimating replacement rate matrices from independent pairwise protein sequence alignments and also carefully studies Muller-Vingron's resolvent method. Comprehensive tests on synthetic datasets show that both new methods perform better than the resolvent method in a variety of settings. The best method is furthermore demonstrated to be robust on small datasets as well as practical on very large datasets of real data. Neither short nor divergent sequence pairs have to be discarded, making the method economical with data. A generalization to multialignment data is suggested and used in a test on protein-domain family phylogenies, where it is shown that the method offers family-specific rate matrices that often have a significantly better likelihood than a general matrix.
Place, publisher, year, edition, pages
2006. Vol. 62, no 6, 663-673 p.
amino acid replacement, protein evolution, general time-reversible model, Markov model, parameter estimation, secondary structure prediction, maximum-likelihood approach, substitution matrices, evolutionary trees, sequence evolution, protein sequences, database, models, families, nucleotide
IdentifiersURN: urn:nbn:se:kth:diva-15728DOI: 10.1007/s00239-004-0113-9ISI: 000238035500001ScopusID: 2-s2.0-33744907021OAI: oai:DiVA.org:kth-15728DiVA: diva2:333770
QC 201005252010-08-052010-08-05Bibliographically approved