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Old 08-13-2011, 12:31 AM   #1
moriah
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Location: Israel

Join Date: Dec 2010
Posts: 23
Red face Mature mirna coordinates

Hi all,

Where can I get coordinates on hg18 of all mature mirna. I've searched the mirbase and ucsc and all I could find was the pre-mir coordinates....

Thanks!
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Old 08-13-2011, 03:57 AM   #2
vebaev
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Location: Plovdiv, Bulgaria

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Default

You can get the matures and map them onto hg18 and easy get their coordinated. If there is non-real mappings you can get only those which are cross-referencing/overlapping with precursor coordinates I guess....

Other way is to look in miRbase there is miRNA.dat file with have coordinates of matures in the precursors. Having precursor coodrinates (gff) you can calculate genomic positions of matures...

I cant remember now any easyer way unfortunately..
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Old 09-15-2011, 01:46 PM   #3
kbhit
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Location: Philadelphia

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Default A tool that should help

I created a tool that will get you the global coordinates. Please contact me using the email address in the readme file if you have any questions.

http://cm.jefferson.edu/index.html
Tool name: miRNACoord (click on Tools & Downloadables to see it)

Last edited by kbhit; 09-16-2011 at 07:54 AM.
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