Question: Getting Pairwise Genome Alignments/Syntenic Regions From Ensembl Or Ucsc?
gravatar for User 9334
7.3 years ago by
User 933460
User 933460 wrote:

This should be trivial but i cannot find the answer on the ensembl website, which just sends the user in circles. i'm trying to download pairwise genome alignments and/or list of syntenic regions (eg between human and mouse) -- without going through any API. the ensembl website refers to various pairwise alignments existing but it all ends up in this link:

where the human/mouse entry in the matrix is broken. how can this data be downloaded? i simply want these files to query what is the alignable region X in human compared with region Y in mouse.... thanks. im open to doing this with ucsc too if it's easier but this information is incredibly difficult to find on either website...

ensembl comparative ucsc • 3.9k views
ADD COMMENTlink written 7.3 years ago by User 933460
gravatar for Bert Overduin
7.3 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

I am afraid Ensembl does not have downloads of pairwise whole genome alignments or syntenic regions available. You really do need the Compara Perl API to retrieve these. If you are not familiar with the API* and also don't have a colleague or bioinformatics department who can help you with this, we gladly see if we can retrieve the data you need for you. To this end, please email us at

As for the broken links in the synteny matrix, thanks for spotting this. The entries in this matrix in fact shouldn't be hyperlinked at all. We will fix these at our earliest convenience.

*It is of course never too late to learn how to use the Ensembl APIs. We regularly organise (free) API workshops, e.g. from 21-23 March at the University of Cambridge.

ADD COMMENTlink written 7.3 years ago by Bert Overduin3.6k
gravatar for Casey Bergman
7.3 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

Pairwise alignments from UCSC (hg19 vs mm9) can be found here:

The Vista team also used to provide nice pairwise human/mouse alignments, but these are now out of date (hg18 vs mm8):

ADD COMMENTlink written 7.3 years ago by Casey Bergman18k

The net format from UCSC is horrendous are there simpler pairwise alignments that can be used between human mouse? Ensembl must have this information somewhere but I cannot find a way to download it. ANy ideas?

ADD REPLYlink written 7.3 years ago by User 933460
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