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Old 10-13-2011, 05:41 AM   #1
koneru_18
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Default How to find closet gene

Hi,

I have multiple genome locations. For a genome location, I need to find nearest gene with its transcription start site on both side.

Can some one help me on this?

thanks
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Old 10-13-2011, 06:36 AM   #2
seqhorn
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If your genome is available at ncbi, ensembl or ucsc you could look up the location there in the genome browser and just zoom out until you see the nearest gene and its TSS. If not, then you have to predict genes in the regions yourself, f.ex. by mapping RNA seqs to the genome or combine with augustus gene prediction software.
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Old 10-13-2011, 06:41 AM   #3
koneru_18
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thanks for your reply....Is there any downloadable file(in any database) which explains gene address, TSS of that gene? then i will map this file with my genome address file by programming.

thanks
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Old 10-13-2011, 06:53 AM   #4
seqhorn
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maybe you can find your genome here and infer TSS from the gene locations

ftp://ftp.ensembl.org/pub/release-64/gtf/
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Old 10-13-2011, 11:33 AM   #5
koneru_18
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thanks...I did not found my solution from the above link.
I repeat..... I have multiple locations from human genomes. I want to determine
what are the closest genes on either side of the location, and if it is in the location how far from the TSS the given location is?

Can some one help me on this??
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Old 10-14-2011, 03:43 AM   #6
GenoMax
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See this link: http://genomewiki.ucsc.edu/index.php...g_nearby_genes

You will also be able to use the table browser tool to refine your search. Look for help on table browser: http://genomewiki.ucsc.edu/index.php...ut_the_Browser

Quote:
Originally Posted by koneru_18 View Post
thanks...I did not found my solution from the above link.
I repeat..... I have multiple locations from human genomes. I want to determine
what are the closest genes on either side of the location, and if it is in the location how far from the TSS the given location is?

Can some one help me on this??
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