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A novel approach to local reliability of sequence alignments.

Schlosshauer, Maximilian and Ohlsson, Mattias LU (2002) In Bioinformatics1998-01-01+01:00 18(6). p.847-854
Abstract
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... (More)
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@thep.lu.se (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Bioinformatics1998-01-01+01:00
volume
18
issue
6
pages
847 - 854
publisher
Oxford University Press
external identifiers
  • wos:000176553400008
  • pmid:12075020
  • scopus:0036305770
ISSN
1367-4803
language
English
LU publication?
yes
id
fbf260e7-d0e7-4636-af7d-f3ddabf7eddc (old id 108907)
alternative location
http://bioinformatics.oxfordjournals.org/cgi/content/short/18/6/847
date added to LUP
2007-07-20 12:48:28
date last changed
2017-08-27 03:54:59
@article{fbf260e7-d0e7-4636-af7d-f3ddabf7eddc,
  abstract     = {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@thep.lu.se},
  author       = {Schlosshauer, Maximilian and Ohlsson, Mattias},
  issn         = {1367-4803},
  language     = {eng},
  number       = {6},
  pages        = {847--854},
  publisher    = {Oxford University Press},
  series       = {Bioinformatics1998-01-01+01:00},
  title        = {A novel approach to local reliability of sequence alignments.},
  volume       = {18},
  year         = {2002},
}