Bioinformatics, Vol 14, 357-366, Copyright © 1998 by Oxford University Press
P Briffeuil, G Baudoux, C Lambert, X De Bolle, C Vinals, E Feytmans and E Depiereux
MOTIVATION: 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. AVAILABILITY: 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'. CONTACT: eric.depiereux@fundp.ac.be
ARTICLES
Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions
Laboratory of Molecular & Structural Biology, The University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. Ye and X. Huang MAP2: multiple alignment of syntenic genomic sequences Nucleic Acids Res., January 7, 2005; 33(1): 162 - 170. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W.-G. Qiu, N. Schisler, and A. Stoltzfus The Evolutionary Gain of Spliceosomal Introns: Sequence and Phase Preferences Mol. Biol. Evol., July 1, 2004; 21(7): 1252 - 1263. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Bakalara, X. Santarelli, C. Davis, and T. Baltz Purification, Cloning, and Characterization of an Acidic Ectoprotein Phosphatase Differentially Expressed in the Infectious Bloodstream Form of Trypanosoma brucei J. Biol. Chem., March 17, 2000; 275(12): 8863 - 8871. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Geetha, V. Di Francesco, J. Garnier, and P. J. Munson Comparing protein sequence-based and predicted secondary structure-based methods for identification of remote homologs Protein Eng. Des. Sel., July 1, 1999; 12(7): 527 - 534. [Abstract] [Full Text] [PDF]
|
|