Ensembl Multiple Genome alignments do not yield the same as pairwise alignments

Question

[except.for.me.and.my.monkey]

Hi everyone! I would like to ask about a problem that emerged when trying to retrieve a genomic region using the multiple genome alignments in Ensembl.

In the past months I could retrieve, using a mouse gene as a query, a complete alignment for the 23 amniota Pecan database. Notably, it yielded two different alignment blocks, one that included only Mouse and Rat, and the other block that included mouse, the remaining 22 species, but did not yield an alignment for Rat in that file. This database has been updated and includes 24 taxa nowadays. When I use as query the same gene, I obtain a successful alignment with only Rat and Mouse, but do not retrieve the other species any more. But, when I compare the same gene with pairwise alignments, I do retrieve the gene sequences for the remaining 22 taxa.

I wanted to ask if there is a way to download all the pairwise alignments, so I could then perform a multiple alignment externally. Besides, if there is a way to obtain this multiple alignment again in Ensembl, I would be interested also to know how to do it.

Cheers,

Diego

Answer 1

[Ensembl Helen]

The 23-way Pecan alignment included 22 species but the alignment was very poor. Essentially only rat was nicely aligned. Now we have an alignment (almost full-length) with rat and spretus. We believe this to be more accurate. The new EPO alignment has a quite different set of species (lost marmoset, vervet, orangutan; gained spretus, macaque, baboon, cow, sheep, pig, dog, horse) but it now covers more orders.

To answer your question, we have the alignments available on our ftp site: ftp://ftp.ensembl.org/pub/release-86/maf/ensembl-compara/

The previous multiple alignments are available here, though we do not have all the pairwise alignments available: ftp://ftp.ensembl.org/pub/release-85/maf/ensembl-compara/

Hope this helps

Helen