title: Incorporating background frequency improves entropy-based residue conservation measures.
abstract: BACKGROUND
  Several entropy-based methods have been developed for scoring sequence conservation in protein multiple sequence alignments. High scoring amino acid positions may correlate with structurally or functionally important residues. However, amino acid background frequencies are usually not taken into account in these entropy-based scoring schemes.
  
  
  RESULTS
  We demonstrate that using a relative entropy measure that incorporates amino acid background frequency results in improved performance in identifying functional sites from protein multiple sequence alignments.
  
  
  CONCLUSIONS
  Our results suggest that the application of appropriate background frequency information may lead to more biologically relevant results in many areas of bioinformatics.
authors.affiliation: Computational Genomics Group, Department of Microbiology, University of Washington, USA. dna@u.washington.edu
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Ram
authors.initials: R
authors.lastname: Samudrala
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D017124:Conserved Sequence; D030562:Databases, Protein; D019277:Entropy; D017433:Protein Structure, Secondary; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*