Overview of different approaches for identifying orthologous regions in two genomes.

<p>Sequence-based methods (e.g. ENSEMBL Compara) start with short local alignments that are extended to longest possible alignments over gaps. Breakpoint-based methods use orthologous elements (called ‘anchors') to find the minimum number of rearrangements that transforms one genome into the other. Positional orthology tries to distinguish orthologs from paralogs by analyzing gene neighborhoods.