What human genome assembly and coordinate system is Ensembl using?
Ensembl uses a one-based coordinate system, whereas UCSC uses a zero-based coordinate system.
Ensembl uses the most recently updated human genome housed at the GRC. This current major assembly release is called GRCh38. NCBI and UCSC use the same genome. UCSC refers to the recent human genome as GRCh38/hg38.
We maintain a long-term archive of the previous assembly of the human genome, GRCh37, with BLAST/BLAT, VEP and BioMart. The data in this archive is based on the Ensembl 75 data.
Linking back to a previous Ensembl release:
If you are looking for older assemblies, try the Ensembl archive sites. In addition to the previous GRCh37, Ensembl release 54 contains the older human assembly NCBI36, which is referred as NCBI36/hg18 by UCSC.
To link to a specific Ensembl archive site, remember to use the Permanent Link (found at the bottom left of each page) eg. http://jun2013.archive.ensembl.org/Homo_sapiens/Info/Index.
Finding the new coordinates for your region of interest
You may have stored a genomic location on NCBI36 or GRCh37, and want to know where the equivalent region is on GRCh38. You can convert old coordinates to new ones via our Rest API or you find the new coordinates by simply adding the old assembly name into the address bar on the Ensembl browser webiste. See an example below:
www.ensembl.org/Homo_sapiens/Location/View?db=core;r=13:32889611-32973805;a=ncbi36.
This will redirect you to the new region in the latest assembly
Assembly updates
The GRC will produce minor assembly releases to GRCh38 on a regular basis. We incorporate these assembly updates, known as "patches" into GRCh38, as we did for GRCh37. By default, the chromosome coordinates do not change when we update the human assembly to the most recent minor release. Instead, we're adding additional alternate sequences to the assembly that can be swapped in on request.
When we update GRCh38 to the latest patch release, the assembly name is appended with the patch number. For example, the first minor assembly release to become available for GRCh38 will be called GRCh38.p1.
If you have any other questions about Ensembl, please do not hesitate to contact our HelpDesk. You may also like to subscribe to the developers' mailing list.