Comparative genomics: from evolution to function

General info

Date 

27 Jun 2011 - 01 Jul 2011 

Location

Utrecht

Website

http://www.nbic.nl/index.php?id=638

Keywords

sequence analysis, protein-protein interaction, pathways, genomics,

Teacher(s)

Snel, Berend Dr.

Huynen, Martijn A. Prof. dr.

Heringa, Jaap Prof. dr.

Contact(s)

Gelder, van Celia Dr.

Description

Genomics data give a comprehensive, but one dimensional and often rather noise image of the cell. Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology, orthology and similarities arising by chance. Moreover it is important to know the assumptions andheuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why they fail (or misdetect) as a consequence of a variety of biological /evolutionary causes. 

The first two days of the course provide a basis for the course with the aim to move "beyond blast" in terms of more sensitive homology searches, domain level analysis of protein evolution as well as morefine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology).This foundation is used to discuss in the three following days in more detail three topics: (1) the study of  functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements. 

The course is intended for PhD students and master students in bioinformatics, especially those interested in evolution and/or those who want to compare various genomics data between species.Participants are expected to have some hands on experience with blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains.