Synteny

Synteny is the conserved order of aligned genomic blocks between species. It is calculated from the pairwise genome alignments created by Ensembl, when both species have a chromosome-level assembly.

The search is run in two phases:

1. We search for alignment blocks that are in the same order in the two genomes. Syntenic alignments that are closer than 200 kb are grouped into a synteny block.
2. Groups that are in synteny are linked, provided that no more than two non-syntenic groups are found between them and they are less than 3 Mb apart.

To avoid overly sparse syntenic views, a synteny dataset may be excluded if it has average genomic coverage below a threshold, typically 5%.