title: Sequence harmony: detecting functional specificity from alignments.
abstract: Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww.
authors.affiliation: Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.
authors.forename: K Anton
authors.initials: KA
authors.lastname: Feenstra
authors.forename: Walter
authors.initials: W
authors.lastname: Pirovano
authors.forename: Klaas
authors.initials: K
authors.lastname: Krab
authors.forename: Jaap
authors.initials: J
authors.lastname: Heringa
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D026901:Membrane Transport Proteins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D000596:Amino Acids; D026901:Membrane Transport Proteins; D011506:Proteins