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Old 08-13-2012, 12:34 PM   #1
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Location: Bethesda, MD

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Default Genome annotation program/script?

Hi, all - I'm looking for a way to annotate a list of positions in a genome. Basically, I have a list of positions that looks like this:

chr1 3026294
chr1 30175158
chr2 17717521

...and so on. I want to know:
1) the names of the gene(s) (if any) that overlap that position
2) the orientation of those genes, and
3) which part of the gene the listed position is (5' UTR, second exon, fourth intron, etc.).

I feel like someone must have made something to do this before, but I don't know where to look. Any ideas? Thanks!
mlafave is offline   Reply With Quote
Old 08-15-2012, 03:41 AM   #2
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Try Bedtools.

You'll need an annotation of course.

Galaxy is also good - see the interval functions there.
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Old 08-19-2012, 05:37 PM   #3
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snpEff is good to, very simple to use
adaptivegenome is offline   Reply With Quote
Old 08-20-2012, 07:17 AM   #4
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I would suggest diffReps. There is a script named
It could read bed format files and generate annotated files fitting most your demands.
The output looks like:
Chrom Start End GName TName Strand TSS TES Feature D2TSS
chr1 2986341 2986690 Ust NM_001108458 - 2868195 3158231 Genebody 171715.5

Refseq and ensembl annotation surpported, but only human, mouse, rat genomes available now.
ishmael is offline   Reply With Quote
Old 08-20-2012, 06:29 PM   #5
Location: Taiwan

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You can try VarioWatch ( It should be able to provide what you want with graphical output in real time. By using "Query by Bacth" can give you results for multiple positions. If you have thousands of positions to query then you can use MegaQuery.

VarioWatch only supports human genome.
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Old 08-24-2012, 04:59 AM   #6
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Thanks for your help, everyone!
mlafave is offline   Reply With Quote

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