title: The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  This paper presents the mathematical details underlying the compositional adjustment of amino acid or DNA substitution matrices.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA.
authors.forename: Yi-Kuo
authors.initials: YK
authors.lastname: Yu
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Altschul
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000596:Amino Acids / Q000032:analysis / Q000737:chemistry*; D008969:Molecular Sequence Data; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D000596:Amino Acids; D011506:Proteins