[ensembl-dev] Question about missing regions in whole genome alignments

[Marc P. Hoeppner]

Dear EnsEMBL developers,

I've noticed that there could be a problem with certain whole genome 
alignments in the current (E82) version of EnsEMBL.

Specifically, for the human region 17:58663933-58739040 (and possibly 
others).

This region is syntenic on all primate genomes (8 primates EPO) as well 
as 23 amniotes (amniotes Pecan). However, in 17 mammals (EPO), this 
region is only identified as syntenic between human and cat - which I 
suspect is a mistake. I understand that Pecan and EPO use different 
algorithms, but the gene in this region (TEX14) is conserved across all 
mammals (and most vertebrates) and has no obvious homologs that may 
explain off-target alignments.

Regards,

Marc