Synteny

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

This is done 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%.

For some synteny datasets, analysis parameters may have been tuned to account for differences in the underlying data such as genome size and evolutionary distance.

Information on any current synteny data is listed alongside available alignments.