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Old 04-11-2013, 05:32 AM   #1
gooday23
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Default Any tool can be fed a list of genome locations and output annotations?

I have a bunch of genome locations and I want to find out what they are. For example, are they located in known genes or non-coding RNA regions or some others. Anyone could suggest me a tool that can be fed in locations and give me a list of annotation?

Thank you very much!
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Old 04-11-2013, 06:01 AM   #2
d1antho
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SNPdat sounds like it would ideal for the task (http://code.google.com/p/snpdat/).

It simply takes as input a tab-delimited file with chr, genomic location and mutation (If you dont have mutations you can always just set this to A,T,C or G and ignore the sequence annotations if performs). Then you just need an annotation file in GTF and a FASTA file. It will annotate locations/SNPs to any feature in the GTF (such as genes/exons/CDS etc) that contains the location. If your SNP/location occurs outside of a feature it will tell you if it is intergenic or intronic and return information on the nearest features and genes (and more!).
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Old 04-11-2013, 06:36 AM   #3
aggp11
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You could also use intersectBed from Bedtools (http://bedtools.readthedocs.org/en/l...intersect.html). You will need your location BED file (chr, start, stop) and an annotation GTF/GFF/BED file from a source like GENCODE (http://www.gencodegenes.org/releases/15.html)

Hope this helps!
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Old 04-12-2013, 04:19 AM   #4
gooday23
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Thank you~ I will have a try~
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Old 04-12-2013, 04:19 AM   #5
gooday23
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It works really well. Thanks!
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