Annotation Of Genomic Regions

Question

[Ezhil La]

Hi,

I would like to annotate the genomic regions in the following format.

chr8:136637189-136638320;
chr3:31496781-31497219

Is there any online tools that I can use to get the near by gene for these regions?

Thanks in advance, Ezhil

Answer 1

[JC]

In the UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway first select your region, then select "Tables" and select the "positions" in "region" choosing "Known Genes" as "table".

In BioMart http://www.ensembl.org/biomart you can select your region defining the chromosome and coordinates adding as much information as you need.

Answer 2

[Alex Paciorkowski]

Lots of options, UCSC browser probably leading the list. I also like to use GEDI. If you enter your region in "coordinate search" multiple annotations from multiple sites are pulled for you, including from UCSC. Sort of one-stop shopping for annotations.

Answer 3

[Sean Davis]

I'd suggest giving the tools on the Galaxy server a try.

Answer 4

[luca.zammataro]

Hello Ezhil, you can try this online annotation tool http://cru.genomics.iit.it/AnnotateGenomicRegions/annotate.jsf Luca

Answer 5

[EagleEye]

http://homer.ucsd.edu/homer/ngs/annotation.html

http://bejerano.stanford.edu/great/public/html/