Ensembl multigenome alignment

Question

[biolab]

Hi everyone,

I would like to download the multi-genome sequence alignment data stored in Ensembl. However, on Biomart I can't find a proper link. Could anyone help with this? Thanks a lot.

[Emily]

BioMart is gene-centric so you can't get genome alignments through that. Are you looking for alignments for particular regions or the whole thing?

[biolab]

Hi, Emily_Ensembl, Thanks, I think I am asking the right person. I am looking for the whole thing actually, but if Ensemble collected the alignments for particular regions (eg. UTRs, CDS), I think it's very useful for my work. Could you please give me some helps or suggestions? Thanks a lot!

Answer 1

[Emily]

We have flat files of the alignments on our FTP site here.

For more specific regions you might want to look at the Ensembl Perl API. There's an online course on using the API here - you'll want to look at the Core section for basics on how to use the API, plus the Compara alignments section. Alternatively, you can use the REST API to get alignments.

[biolab]

Hi Emily_Ensembl, thanks a lot for your helps. They are really helpful!