[ensembl-dev] Compara: Incosistent results in LastZ alignments?

[Marc P Hoeppner]

Dear EnsEMBL team,

I have been using LastZ alignments to check for locus conservation 
between human and mouse. However, I have come across an issue that seems 
to be related to the inclusion of ALT loci in the alignments.

Specifically, when comparing human<->mouse for the human snoRNA 
ENSG00000200222, I get the mouse U3 snoRNA ENSMUSG00000097846 as the 
matching locus. However, this annotation sits on an ALT assembly. When I 
do the comparison in reverse (mouse<->human), the mouse U3 snoRNA aligns 
to the human locus  ENSG00000212211 (same chromosome as the original 
human U3 query, but 4 Mbp off).

I suppose that shouldn't happen and may be related to these snoRNAs 
being repetetive sequences. Still, I qould have guessed that the gneomic 
context (i.e. neighboring coding genes) should provide some guidance to 
how these loci ought to be aligned? Is this a LastZ problem? Wouldn't it 
perhaps be more sensible to exclude ALT assemblies until these 
alignments can be represented as graphs rather than flattened pairwise 
comparisons?

Kind regards,

Marc