By Topic

In?uenza-specific Amino Acid Substitution Model

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$33 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

3 Author(s)
Dang Cao Cuong ; Coll. of Technol., Vietnam Nat. Univ. Hanoi, Hanoi, Vietnam ; Le Si Quang ; Le Sy Vinh

Amino acid substitution model is a crucial component in protein sequence comparative systems such as protein sequence similarity searching, protein sequence alignment, and protein phylogenetic analysis. Although several general amino acid substitution models have been estimated from large protein databases, they might not be appropriate for analyzing specific species. In this paper, we apply the maximum likelihood approach to all influenza protein sequences to estimate an amino acid substitution model of so-called I09 for influenza viruses. Comparing I09 with fourteen other widely used models, we achieve remarkable results: (1) a likelihood improvement of phylogenetic trees based on I09 compared with other models. Precisely, I09 results in the best likelihood in 436 out of 489 cases tested; (2) tree topologies constructed with I09 and other models are frequently different indicating that the impact of I09 is not only on the likelihood improvement but also in tree topologies; (3) marked differences between I09 and other models revealing that existing models are not be able to capture the amino acid substitution process of influenza viruses.

Published in:

Knowledge and Systems Engineering, 2009. KSE '09. International Conference on

Date of Conference:

13-17 Oct. 2009