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Photo of Mattias Ohlsson

Mattias Ohlsson

Professor

Photo of Mattias Ohlsson

A novel approach to local reliability of sequence alignments.

Author

  • Maximilian Schlosshauer
  • Mattias Ohlsson

Summary, in English

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 [dot] lu [dot] se

Department/s

  • Computational Biology and Biological Physics - Undergoing reorganization

Publishing year

2002

Language

English

Pages

847-854

Publication/Series

Bioinformatics

Volume

18

Issue

6

Document type

Journal article

Publisher

Oxford University Press

Topic

  • Bioinformatics and Systems Biology

Status

Published

ISBN/ISSN/Other

  • ISSN: 1367-4803