title: Comparative analysis of multiple protein-sequence alignment methods.
abstract: We have analyzed a total of 12 different global and local multiple protein-sequence alignment methods. The purpose of this study is to evaluate each method's ability to correctly identify the ordered series of motifs found among all members of a given protein family. Four phylogenetically distributed sets of sequences from the hemoglobin, kinase, aspartic acid protease, and ribonuclease H protein families were used to test the methods. The performance of all 12 methods was affected by (1) the number of sequences in the test sets, (2) the degree of similarity among the sequences, and (3) the number of indels required to produce a multiple alignment. Global methods generally performed better than local methods in the detection of motif patterns.
authors.affiliation: Department of Biological Sciences, University of Nevada, Las Vegas 89154-4004.
authors.forename: M A
authors.initials: MA
authors.lastname: McClure
authors.forename: T K
authors.initials: TK
authors.lastname: Vasi
authors.forename: W M
authors.initials: WM
authors.lastname: Fitch
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D010450:Endopeptidases / Q000737:chemistry; D006454:Hemoglobins / Q000737:chemistry; D008969:Molecular Sequence Data; D010770:Phosphotransferases / Q000737:chemistry; D017434:Protein Structure, Tertiary; D016914:Ribonuclease H / Q000737:chemistry; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D006454:Hemoglobins; D010770:Phosphotransferases; D016914:Ribonuclease H; D010450:Endopeptidases