CREx: inferring genomic rearrangements based on common intervals

CREx: inferring genomic rearrangements based on common intervals

SUMMARY We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals and tandem-duplication-random-loss (TDRL) events. It supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based on common intervals, which reflec...

Inferring Positional Homologs with Common Intervals of Sequences

Inferring orthologous and paralogous genes is an important problem in whole genomes comparisons, both for functional or evolutionary studies. In this paper, we introduce a new approach for inferring candidate pairs of orthologous genes between genomes, also called positional homologs, based on the conservation of the genomic context. We consider genomes represented by their gene order – i.e. se...

On Common Intervals with Errors

The information that groups of genes co-occur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene clusters, has led to various models of increasing generality. A central feature to enhance the biological relevance of their definition when applied to real genomic data is to allow for slight differences ...

Genomic Rearrangements and Evolution

Approximate common intervals based gene cluster models