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Bioinformatics Vol. 18 no. 6 2002
Pages 847-854
© 2002 Oxford University Press

A novel approach to local reliability of sequence alignments

Maximilian Schlosshauer and Mattias Ohlsson

Complex Systems Division, Department of Theoretical Physics, University of Lund, Sölvegatan 14A, S–223 62 Lund, Sweden

Received on August 14, 2001 ; revised on January 14, 2002 ; accepted on January 21, 2002

Motivation: The pairwise alignment of biological sequences obtained from an algorithm will in general contain both correct and incorrect parts. Hence, to allow for a valid interpretation of the alignment, the local trustworthiness of the alignment has to be quantified.

Results: We present a novel approach that attributes a reliability index to every pair of residues, including gapped regions, in the optimal alignment of two protein sequences. The method is based on a fuzzy recast of the dynamic programming algorithm for sequence alignment in terms of mean field annealing. An extensive evaluation with structural reference alignments not only shows that the probability for a pair of residues to be correctly aligned grows consistently with increasing reliability index, but moreover demonstrates that the value of the reliability index can directly be translated into an estimate of the probability for a correct alignment.

Contact: mattias{at}thep.lu.se


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