Improving the performance of positive selection inference by filtering unreliable alignment regions.

Détails

ID Serval
serval:BIB_21BBC77DDD25
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Improving the performance of positive selection inference by filtering unreliable alignment regions.
Périodique
Molecular Biology and Evolution
Auteur(s)
Privman E., Penn O., Pupko T.
ISSN
1537-1719 (Electronic)
ISSN-L
0737-4038
Statut éditorial
Publié
Date de publication
2012
Peer-reviewed
Oui
Volume
29
Numéro
1
Pages
1-5
Langue
anglais
Notes
Privman E., Penn O. contributed equally
Résumé
Errors in the inferred multiple sequence alignment may lead to false prediction of positive selection. Recently, methods for detecting unreliable alignment regions were developed and were shown to accurately identify incorrectly aligned regions. While removing unreliable alignment regions is expected to increase the accuracy of positive selection inference, such filtering may also significantly decrease the power of the test, as positively selected regions are fast evolving, and those same regions are often those that are difficult to align. Here, we used realistic simulations that mimic sequence evolution of HIV-1 genes to test the hypothesis that the performance of positive selection inference using codon models can be improved by removing unreliable alignment regions. Our study shows that the benefit of removing unreliable regions exceeds the loss of power due to the removal of some of the true positively selected sites.
Mots-clé
multiple sequence alignment, GUIDANCE, alignment reliability, positive selection, molecular evolution, phylogeny
Pubmed
Web of science
Open Access
Oui
Création de la notice
20/07/2011 13:04
Dernière modification de la notice
20/08/2019 12:58
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