Dynamic programming alignment accuracy.
J Comput Biol
; 5(3): 493-504, 1998.
Article
em En
| MEDLINE
| ID: mdl-9773345
Algorithms for generating alignments of biological sequences have inherent statistical limitations when it comes to the accuracy of the alignments they produce. Using simulations, we measure the accuracy of the standard global dynamic programming method and show that it can be reasonably well modelled by an "edge wander" approximation to the distribution of the optimal scoring path around the correct path in the vicinity of a gap. We also give a table from which accuracy values can be predicted for commonly used scoring schemes and sequence divergences (the PAM and BLOSUM series). Finally we describe how to calculate the expected accuracy of a given alignment, and show how this can be used to construct an optimal accuracy alignment algorithm which generates significantly more accurate alignments than standard dynamic programming methods in simulated experiments.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Alinhamento de Sequência
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
J Comput Biol
Assunto da revista:
BIOLOGIA MOLECULAR
/
INFORMATICA MEDICA
Ano de publicação:
1998
Tipo de documento:
Article