Question: prediction
akbar...@yahoo.com
In UCSC in "Genes and Gene Predictions" group there are track of "miRNA" prediction for human genome assembly, But there are not this track for other species how can we get same information for other species?
Regards
Mahboubeh Akbari
Christopher Lee
Hi Mahboubeh
Thank you for your question regarding miRNA data on other species.
We do not plan on adding an miRNA track to any other species in the near future. However, you
can extract miRNA data from the Ensembl gene tracks, if your organism of interest has the
Ensembl track.
To get miRNA data out of the Ensembl track, follow the below Table Browser steps:
1. Head to the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables
2. Select your organism of interest from the clade, genome, and assembly dropdowns.
3. In the "group", "track", and "table" dropdowns select "Genes and Genes Predictions",
"Ensembl Genes", and "ensGene".
4. Next to "filter" click the "create" button.
5. On the filters page, check the box next to "ensemblSource" and then click
"allow filtering using fields in checked tables".
6. There should now be a new section called: "abcDef.ensemblSource based filters" where abcDef
is your organism of interest. In the text box next to "source", type "miRNA".
7. Click the "submit" button.
8. Enter any position info if applicable, choose your output format, then click "get output".
You will now have a list of gene identifiers annotated as miRNA by Ensembl. Please let
us know if your organism of interest does not have the Ensembl track, or your organism
of interest is not one of the assemblies with miRNA track.
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
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