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Construction of Amino-Acid Substitution Matrix of Archaea Domain

Author: HanGang
Tutor: TaoShiZuo
School: Northwest University of Science and Technology
Course: Biochemistry and Molecular Biology
Keywords: sequence alignment amino acid substitution probability archaea content odds
CLC: Q936
Type: Master's thesis
Year: 2011
Downloads: 7
Quote: 0
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Abstract


As an important method in constructing phylogenic trees and annotating protein functions, alignment of amino acid sequences would profoundly influence the estimation about an amino acid substitution event which occurred alone the evolution. We speculate the most probable type of substitution in understanding the probability of occurrence of each substitution event to determine the most believable alignment result. In order to get the probability of all types of amino acid substitution events, we accumulated 13413 substitution events that occurred in 40 species in which 3980 amino acid sequences were studied, and the amino acid substitution matrix were constructed based on the original statistical matrix. In this study, the whole research data was limited in archaea to examine whether a difference exists between substitution patterns in different domains. Archaea is a kind of particularly special species group which mostly live in extreme ecological environments. The result indicates that a certain kind of difference of amino acid substitution matrix emerged between archaea and the whole biosphere which was described in the study of Dayhoff 1978.Meanwhile,this study firstly found that the content odds of amino acids plays significant role in constructing amino acid substitution matrix and describing amino acid substitution ability.

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CLC: > Biological Sciences > Microbiology > Microbial biochemistry
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