Identifying Site-Specific Substitution Rates
نویسندگان
چکیده
منابع مشابه
Identifying site-specific substitution rates.
A maximum likelihood framework for estimating site-specific substitution rates is presented that does not require any prior assumptions about the rate distribution. We show that, when the branching pattern of the underlying tree is known, the analysis of pairs of positions is sufficient to estimate site-specific rates. In the abscense of a known topology, we introduce an iterative procedure to ...
متن کاملToo packed to change: side-chain packing and site-specific substitution rates in protein evolution
In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates are solvent accessibility and packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between a site's C α and the C α of...
متن کاملToo packed to change: site-specific substitution rates and side-chain packing in protein evolution
In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates is packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between the site’s Cα and the other Cα . According to a mechan...
متن کاملInferring Site-Specific Evolutionary Rates: Bayesian Methods are Superior
Not all sites in protein sequences evolve at the same rate during the course of evolution. The working hypothesis assumes that evolutionary conserved sites in a protein sequence point to functionally important regions. Thus, identifying conserved regions in a protein impacts such areas as functional annotation studies, drug design, quaternary structure prediction, and protein biochemistry [1]. ...
متن کاملSynonymous substitution rates in enterobacteria.
It has been shown previously that the synonymous substitution rate between Escherichia coli and Salmonella typhimurium is lower in highly than in weakly expressed genes, and it has been suggested that this is due to stronger selection for translational efficiency in highly expressed genes as reflected in their greater codon usage bias. This hypothesis is tested here by comparing the substitutio...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2003
ISSN: 0737-4038,1537-1719
DOI: 10.1093/molbev/msg019