Bayesian analysis of amino acid substitution models
نویسندگان
چکیده
منابع مشابه
Bayesian analysis of amino acid substitution models.
Models of amino acid substitution present challenges beyond those often faced with the analysis of DNA sequences. The alignments of amino acid sequences are often small, whereas the number of parameters to be estimated is potentially large when compared with the number of free parameters for nucleotide substitution models. Most approaches to the analysis of amino acid alignments have focused on...
متن کاملAmino Acid Substitution Scores
GNPKVKAH Here we discuss standard ways of assigning a score to each amino acid pair, i.e., to each possible column of a gap-free pairwise protein alignment. Examples of such scoring matrices include the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other informatio...
متن کاملAmino Acid Substitution Scores
GNPKVKAH Here we discuss standard ways of assigning a score to each amino acid pair, i.e., to each possible column of a gap-free pairwise protein alignment. Examples of such scoring matrices include the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other informatio...
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The BLOSUM (BLOck SUbstitution Matrices) matrices were derived by Steven and Jorja Henikoff in 1992 1. They were based on a much larger data set than the PAM matrices, and used conserved local alignments or “blocks,” rather than global alignments of very closely related sequences. In order to account for different degrees of sequence divergence, the Henikoffs used clustering rather than an expl...
متن کاملAmino Acid Substitution Matrices
• Biophysical properties of residues: Amino acids differ in size and charge. Some are acidic, some are basic, some have aromatic side chains. Generally, replacement of an amino acid with another amino acid with similar properties is less likely to break the protein or cause dramatic changes in function than replacement with an amino acid with different properties. A substitution matrix should r...
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ژورنال
عنوان ژورنال: Philosophical Transactions of the Royal Society B: Biological Sciences
سال: 2008
ISSN: 0962-8436,1471-2970
DOI: 10.1098/rstb.2008.0175