Laboratory of Computational and Quantitative Biology (LCQB)
UMR 7238 CNRS - Sorbonne Université
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Modeling protein evolution
Date:
Monday, January 30, 2012 - 00:00
Speaker:
Olivier Gascuel
Address:
Campus Jussieu
place Jussieu 75005 Paris Métro Jussieu
Amphithéâtre 45A - tour 45 4
Affiliation:
Méthodes et Algorithmes pour la Bio-informatique LIRMM - CNRS
Abstract:
I’ll describe our recent efforts to model protein evolution and amino-acid substitutions by (1) designing an easy to use pipeline to estimate amino-acid replacement matrices for specific protein groups, (2) using the knowledge of the protein structure, when available, (3) simplifying mixture models that have been proposed so far.
References:
Dang C. C.., Lefort V., Le V. S., Le Q. S., Gascuel O. “ReplacementMatrix: a Web Server for Maximum Likelihood Estimation of Amino Acid Replacement Rate Matrices", Bioinformatics, 2011 [Epub ahead of print].
LE S.Q., GASCUEL O. “Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics is Clearly Beneficial”, Systematic Biology, 59:277-87, 2010.
Le SQ., Lartillot N., Gascuel O. “Phylogenetic mixture models for proteins”. Philosophical Transactions of the Royal Society - Biological Science B, 363(1512): 3965-3976, 2008.
Le SQ., Gascuel O. “An improved general amino acid replacement matrix”. Molecular Biology and Evolution 25(7):1307-20, 2008.
Type:
Interdisciplinary Seminar
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