GeneSyn: a tool for detecting conserved gene order across genomes

GeneSyn is a software tool that allows automatic detection of conserved gene order from annotated genomes. The increasing amount of available genome data makes it possible now to shed light on the molecular dynamics shaping their evolution. Genome evolution not only involves changes at the sequence level with base substitutions and/or insertion/deletion events but also rearrangements of the gene order along the genome. Comparative analysis of gene order in multiple genomes may help in investigating general or lineage-specific genome plasticity as well as in the inference of phylogenetic relationships. In particular, investigation of gene contiguity on a chromosome (sometimes improperly referred to as conserved gene synteny), even if sometimes interrupted by intervening genes, suggests a functional coupling. We present here an algorithm and software to detect gene strings conserved in at least a given fraction of input genomes and present a simple example application in animal mitochondrial gene order