In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction.

Abstract : The increase in the number of entirely sequenced genomes makes increasingly accurate the study of the mechanisms of evolution through the comparison of contemporary genomes. One of the main problems is to reconstruct plausible ancestral genome architecture, which furnishes hypotheses about both the history of contemporary genomes and the general mechanisms of their formation. While not all methods for the ancestral reconstruction necessarily converge towards the same results, they are all based on the same three steps: identification of common markers in contemporary genomes, construction of comparative maps for these genomes, and reconciliation of these maps under a maximum parsimony criterion. The quantity of data that must be analyzed requires the automation of processing and meeting these needs induces great computational challenges. Through refinement of computational models and methods, we can obtain more biologically relevant hypotheses by adding biological constraints. In this thesis, we propose a new method for the identification of common markers to construct comparative maps for evolutionary distant genomes. Next, we apply a new method of ancestral genome reconstruction based on adjacencies of synteny markers and genomic distances between contemporary genomes. Finally, after correcting the existing algorithm for computing an optimal sequence of rearrangements that occured during the evolution of modern genomes from their common ancestor, we propose a new tool called VIRAGE that permits the animated visualization of rearrangement scenarios between species.
Document type :
Theses
Complete list of metadatas

https://tel.archives-ouvertes.fr/tel-00350900
Contributor : Géraldine Jean <>
Submitted on : Wednesday, January 7, 2009 - 5:26:49 PM
Last modification on : Thursday, January 11, 2018 - 6:20:16 AM
Long-term archiving on : Tuesday, June 8, 2010 - 6:59:40 PM

Identifiers

  • HAL Id : tel-00350900, version 1

Citation

Géraldine Jean. In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction.. Other [cs.OH]. Université Sciences et Technologies - Bordeaux I, 2008. English. ⟨tel-00350900v1⟩

Share

Metrics

Record views

34

Files downloads

6