Section: Application Domains

Genome comparison

This application domain aims at providing a global relationship between genomes. The problem lies in the different structures that genomes can have: segments of genome can be rearranged, duplicated or deleted (the alignment can no longer be done in one piece). Therefore one major aim is the study of chromosomal rearrangements, breaking points, structural variation between individuals of the same species, etc. However, even analyses focused on smaller variations such as Single Nucleotide Polymorphisms (SNP) at the whole genome scale are different from the sequence comparison problem, since one needs first to identify common (orthologous) parts between whole genome sequences and thus obtain this global relationship (or map) between genomes. New challenges in genome comparison are emerging with the evolution of sequencing techniques. Nowadays, they allow for comparing genomes at intra-species level, and to deal simultaneously with hundreds or thousands of complete genomes. New methods are needed to find the sequence and structural variants between such a large number of non-assembled genomes. Even for the comparison of more distant species, classical methods must be revisited to deal with the increasing number of genomes but more importantly their decreasing quality: genomes are no longer fully assembled nor annotated.