title: Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions.
abstract: BACKGROUND
  The prediction reliability of seven multiple alignment servers currently available on the Internet (ClustalW, MAP, PIMA, Block Maker, MSA, MEME and Match-Box) has been evaluated in terms of power (sensitivity) and confidence (selectivity). Therefore, the alignments obtained have been respectively compared to refined structural alignments for 20 families of related proteins with low levels of identity.
  
  
  RESULTS
  Results clearly show that any powerful method remains reliable when the rate of identity falls. For some methods, power and confidence decrease linearly with the rate of identity, while other methods emphasize reliability at the cost of a lower power. Increasing the number of related sequences included in the alignment may either improve or decrease the quality of the predictions substantially. For some methods, the gain in power or in confidence is quite systematic; for others, the effect of the addition of homologous sequences is highly unpredictable. Extracting the consensus between two different methods may increase the overall confidence of the predictions tremendously. Our conclusions induce users of sequence alignment methods on the Internet to select the most suitable technique according to their requirements in terms of selectivity and sensitivity.
  
  
  BACKGROUND
  The aligned sequences of the 20 alignments of structure can be obtained automatically by sending the message 'send: cabios_tests.txt' by e-mail to 'matchbox@biq.fundp.ac.be'.
  
  
  BACKGROUND
  eric.depiereux@fundp.ac.be
authors.affiliation: Laboratory of Molecular & Structural Biology, The University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium.
authors.forename: P
authors.initials: P
authors.lastname: Briffeuil
authors.forename: G
authors.initials: G
authors.lastname: Baudoux
authors.forename: C
authors.initials: C
authors.lastname: Lambert
authors.forename: X
authors.initials: X
authors.lastname: De Bolle
authors.forename: C
authors.initials: C
authors.lastname: Vinals
authors.forename: E
authors.initials: E
authors.lastname: Feytmans
authors.forename: E
authors.initials: E
authors.lastname: Depiereux
mesh_terms: D003195:Computer Communication Networks; D003657:Decision Making; D005069:Evaluation Studies as Topic; D009862:Online Systems; D012091:Repetitive Sequences, Nucleic Acid; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment