COMPUTER SYSTEM FOR ANALYSIS OF MOLECULAR EVOLUTION MODES OF PROTEIN-CODING GENES (SAMEM): RELATION OF MOLECULAR EVOLUTION WITH THE PHENOTYPICAL FEATURES OF ORGANISMS
https://doi.org/10.1234/XXXX-XXXX-2010-4-14-16
Abstract
A web-available computer system for analyzing the molecular evolution modes of genes and proteins was developed (SAMEM: http://pixie.bionet.nsc.ru/samem/). SAMEM computations are based on the ratio of radical to conservative amino acid replacements, on the rate of amino acid changes in the course of protein evolution, and on the statistical relations between evolutionary change of all known amino acid properties and user defined phenotypical features of organisms.
About the Authors
K. V. Gunbin
Институт цитологии и генетики Сибирского отделения РАН, г. Новосибирск
Russian Federation
Russian Federation
M. A. Genaev
Институт цитологии и генетики Сибирского отделения РАН, г. Новосибирск
Russian Federation
Russian Federation
D. A. Afonnikov
Институт цитологии и генетики Сибирского отделения РАН, г. Новосибирск; Новосибирский государственный университет, г. Новосибирск
Russian Federation
Russian Federation
N. A. Kolchanov
Институт цитологии и генетики Сибирского отделения РАН, г. Новосибирск; Новосибирский государственный университет, г. Новосибирск
Russian Federation
Russian Federation
References
1. Drummond D.A., Wilke C.O. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequ¬ence evolution // Cell. 2008. Vol. 134. N 2. P. 341—352.
2. Huang Y., Koonin E.V., Lipman D.J., Przytycka T.M. Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage // Nucleic Acids Res. 2009. Vol. 37. N 20. P. 6799—6810.
3. Zhang J. Rates of conservative and radical nonsynony- mous nucleotide substitutions in mammalian nuclear genes // J. Mol. Evol. 2000. Vol. 50. N 1. P. 56—68.
4. Pupko T., Sharan R., Hasegawa M., Shamir R., Gra- ur D. Detecting excess radical replacements in phylogenetic trees // Gene. 2003. Vol. 319. P. 127—135.
5. Woolley S., Johnson J., Smith M.J., Crandall K.A., McClellan D.A. TreeSAAP: selection on amino acid proper¬ties using phylogenetic trees // Bioinformatics. 2003. Vol. 19. N 5. P. 671—672.
6. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks // Proc. Natl. Acad. Sci. U.S.A. 1992. Vol. 89. N 22. P. 10915—10919.
7. Kawashima S., Pokarowski P., Pokarowska M., Kolins- ki A., Katayama T., Kanehisa M. AAindex: amino acid index database, progress report 2008 // Nucleic Acids Res. 2008. Vol. 36. Database issue. P. D202—D205.
8. Fletcher W., Yang Z. INDELible: a flexible simulator of biological sequence evolution // Mol. Biol. Evol. 2009. Vol. 26. N 8. P. 1879—1888.
9. Gunbin K.V., Afonnikov D.A., Kolchanov N.A. Molecular evolution of the hyperthermophilic archaea of the Pyro- coccus genus: analysis of adaptation to different environmental conditions // BMC Genomics. 2009. Vol. 10. P. 639.
10. Messier W., Stewart C.B. Episodic adaptive evolution of primate lysozymes // Nature. 1997. Vol. 385. N 6612. P. 151—154.
Review
For citations:
Gunbin K.V., Genaev M.A., Afonnikov D.A., Kolchanov N.A. COMPUTER SYSTEM FOR ANALYSIS OF MOLECULAR EVOLUTION MODES OF PROTEIN-CODING GENES (SAMEM): RELATION OF MOLECULAR EVOLUTION WITH THE PHENOTYPICAL FEATURES OF ORGANISMS. Vestnik Moskovskogo universiteta. Seriya 16. Biologiya. 2010;(4):14-16. (In Russ.) https://doi.org/10.1234/XXXX-XXXX-2010-4-14-16
Views:
302
Email this article 