... Ensembl is reviewing how we provide access to pseudoautosomal regions (PAR) in human, and we'd like your input.
Please let us know how our current PAR strategy works for you. What do you like and what is difficult? If our current strategy (explained below) is not working for you, please let us know ...
... BioMart does support hg18 (NCBI36). This functionality can be found by going to the e54 archive site, which Ensembl plans to maintain for at least another year and a half. Find it here:
If you know Perl, you can also access the archive through ...
... You can do this with Ensembl with MySQL:
Consider the display_xref_id rather than going for external synonym.
The external synonym is not always available.
The following query should work:
select distinct stable_id, display_label from gene g, xref x
where x.xref_id = g.display_xref_id
... A few more tips that might help:
The INSDC coordinates are visible on Ensembl gene summary pages like this one http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32889611-32973805
For the primary assembly, chromosome synonyms are here:
... Hi Ning-Yi Shao,
I have a little more information about this for you.
UCSC probably do this because the names that they use are not the officially accepted names.
In most cases, Ensembl does use the official accession.version in the seq_region table. When they don't (for example - all chromosomes ...
... Just to add to this, it is possible through the Ensembl REST, but you have to specify a region:
... BioMart is a useful tool for this, as mentioned.
The Ensembl Core Perl API can also be used to retrieve GO terms.
Installation instructions are here:
Modules are here:
... Ensembl's latest video on our YouTube channel provides a quick guide to installing our APIs.
Check out over 20 videos on Ensembl data and how to access it, including BioMart.
... See the table at the bottom of this view for RefSeqs mapped to Ensembl transcripts:
Using the Perl API, you can find these as 'Xrefs' or External References.
If you want to use the browser, have a look at the v ...