アブストラクト
| Date | July 16, 2010 |
| Speaker | Kimmen Sjölander, Associate Professor, Berkeley Phylogenomics Group, University of California, Berkeley |
| Title | New methods for functional site identification, orthology prediction and multiple sequence alignment |
| Abstract |
Theodosius Dobzhansky, the noted geneticist and evolutionary biologist, is famous for his saying “Nothing makes sense except in the light of evolution.” In this talk, I will discuss the explicit use of evolution as a fundamental principle in bioinformatics, using machine learning methods in combination with evolutionary models to improve the power and specificity of a number of bioinformatics tasks, including phylogenomic methods to predict protein structure and function, identify orthologs, predict enzyme active sites, and estimate accurate multiple sequence alignments and protein superfamily phylogenies and reconstruct species phylogenies. I will describe the PhyloFacts Phylogenomic Encyclopedias (at http://phylogenomics.berkeley.edu/phylofacts/) which provide pre-calculated phylogenies for ~60K protein families and structural domains, with ~1.6M hidden Markov models for classification of new sequences to functional families and subfamilies.
http://phylogenomics.berkeley.edu |