Paper Info
Title
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions.
Abstract
Amino acid substitution matrices play a central role in protein alignment methods. Standard log-odds matrices, such as those of the PAM and BLOSUM series, are constructed from large sets of protein alignments having implicit background amino acid frequencies. However, these matrices frequently are used to compare proteins with markedly different amino acid compositions, such as transmembrane proteins or proteins from organisms with strongly biased nucleotide compositions. It has been argued elsewhere that standard matrices are not ideal for such comparisons and, furthermore, a rationale has been presented for transforming a standard matrix for use in a non-standard compositional context.This paper presents the mathematical details underlying the compositional adjustment of amino acid or DNA substitution matrices.
Year
DOI
Venue
2005
10.1093/bioinformatics/bti070
Bioinformatics
Keywords
Field
DocType
compositional adjustment,standard log-odds matrix,non-standard compositional context,protein alignment method,different amino acid composition,standard matrix,dna substitution matrix,amino acid,amino acid substitution matrix,amino acid frequency,nucleotides,transmembrane protein
Data mining,Amino acid,Biochemistry,Computer science,Matrix (mathematics),DNA,BLOSUM,Transmembrane protein,Nucleotide,Computational biology,Substitution matrix
Journal
Volume
Issue
ISSN
21
7
1367-4803
Citations 
PageRank 
References 
38
2.28
3
Authors
2
Name
Order
Citations
PageRank
Yi-Kuo Yu114014.43
Stephen F Altschul218026.55