Computational Research IIT@SEMM: AnnotateGenomicRegions
Credits: Computational Research IIT@SEMM. Copyright 2011-2014 by IIT@SEMM. All rights reserved. Developed using JSF and PrimeFaces

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Paste your genomic regions and annotate overlapping or neighboring genomic features like:

  • Refgene ID
  • Refgene Symbol
  • Ensgene ID
  • Ensgene Symbol
  • CpG islands
  • promoter regions

No programming skills required. Download output and paste into Excel.

Annotations are downloaded from UCSC Golden Path Genome Browser on a roughly yearly basis.

You can choose to annotate overlaps and/or neighborhoods of your genomic regions.

Overlap mode reports overlapping annotation(s). Overlap annotations are labeled by _ol.

When annotating neighborhoods, two columns are created for each annotation, one holding the left neighbor (labeled _ln) and one holding the right neighbor (labeled _rn).

The results are presented as a download link to a temporary (2 hours) zip file.

To speed up your searches, sort your genomic regions first by chromosome and then by start position. Unsorted genomic regions will be sorted internally, adding some time to execute your query.

AnnotateGenomicRegions is an open source Sourceforge project.

May 2014 release: Latest UCSC annotations, hg38 support, Primefaces 5.0.