title: APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.
abstract: BACKGROUND
  We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods.
  
  
  RESULTS
  Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages.
authors.affiliation: Department of Biochemistry, University College, Cork, Ireland.
authors.forename: Orla
authors.initials: O
authors.lastname: O'Sullivan
authors.forename: Mark
authors.initials: M
authors.lastname: Zehnder
authors.forename: Des
authors.initials: D
authors.lastname: Higgins
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
authors.forename: Aurelien
authors.initials: A
authors.lastname: Grosdidier
authors.forename: Cédric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019985:Benchmarking / Q000379:methods*; D008969:Molecular Sequence Data; D012015:Reference Standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods* / Q000592:standards; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D020539:Sequence Analysis, Protein / Q000379:methods* / Q000592:standards; D017385:Sequence Homology; D012984:Software; D012986:Software Validation