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Question: Mirna Targets At All Transcribed But Not Translated Sites At Genome Level
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gravatar for Abhay Krishna
8.0 years ago by
Abhay Krishna • 70
Abhay Krishna • 70 wrote:
I have an intuitive feeling, It will be possible to do it in Galaxy, to be precise: I want to find all miRNA targets at whole genome level (These targets should be transcribed but not translated), in other words pseudogenes and other non coding rna. Any ideas? How to get this. Best Abhay
galaxy • 699 views
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modified 8.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 8.0 years ago by Abhay Krishna • 70
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gravatar for Jennifer Hillman Jackson
8.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Abhay, To pull in annotation and view/use it in Galaxy, use the "Get Data" tool and either extract from one of the listed databases or load a local file. The primary source for known miRNA data would be: http://www.mirbase.org/. Pseudogenes and other longer non-coding mRNA data can be found in Genbank http://www.ncbi.nlm.nih.gov/genbank/GenbankSearch.html and many other major genome annotation repositories. For Human and other vertebrate species, the UCSC Genome Browser would be a good place to review tracks based on the the sources above. These can be easy imported with the "Get Data -> UCSC main or BX main" tool. If you would like more help with a particular genome or dataset, please let us know, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org
ADD COMMENT • link written 8.0 years ago by Jennifer Hillman Jackson ♦ 25k
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