[Genome] (no subject)

[Archana Thakkapallayil]

Hello Yossy,

To get this information, first you need to BLAT your gene sequence and 
then obtain the coordinates for your gene from the BLAT result. 
Information on doing BLAT is here:

http://genome.cse.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

You could then use the Table Browser to get information on the miRNAs 
that fall within your gene coordinates. To do this, click on the 
"Tables" link in the blue bar at the top of the Genome Browser page.  
Then make the following selections:

clade: vertebrate
genome: Human
assembly: Mar. 2006
group: Genes and Gene Prediction Tracks
track: sno/miRNA
table: wgRna
region: position
paste your gene coordinates into the position text box.

You could than choose the output format that you are interested in and 
hit "get output" button.

This gives you the list of miRNAs that align within your gene sequence.

If you are interested in doing a batch BLAT job, you could download the 
command line Blat. It is free for personal,academic and non-profit 
institution use. You can find the details regarding downloading the Blat 
program here:

http://genome.ucsc.edu/FAQ/FAQblat#blat3

This link tells you how to replicate the parameters used in the 
web-based Blat:

http://genome.ucsc.edu/FAQ/FAQblat

I hope that this is helpful to you. Please let us know if you have 
further questions.

Regards,

Archana
UCSC Genome Bioinformatics Group


yossy wrote:
> hello,
>
> how can i find miRNA targets in my gene sequence ?
>
> thanks,
> best
>
> Yossy Machluf
> Department of Molecular Cell Biology
> The Weizmann Institute of Science
> Rehovot 76100, ISRAEL
> Phone: 972-8-934-6097
> Fax: 972-8-934-4125
> Mail: machluf.yossy at weizmann.ac.il
>
> _______________________________________________
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>