A novel approach to local reliability of sequence alignments.
Schlosshauer, Maximilian and Ohlsson, Mattias LU
(2002)
In Bioinformatics
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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/108907
- author
- Schlosshauer, Maximilian
and Ohlsson, Mattias
LU
- organization
- publishing date
- 2002
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Bioinformatics
- 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
- 2016-04-01 11:50:00
- date last changed
- 2024-03-25 15:25:31
@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 = {{Bioinformatics}},
title = {{A novel approach to local reliability of sequence alignments.}},
url = {{http://bioinformatics.oxfordjournals.org/cgi/content/short/18/6/847}},
volume = {{18}},
year = {{2002}},
}