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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The Annotate option permits annotating your regions with some of the annotations that are frequently requested by biologists. These annotations are downloaded form the UCSC genome browser, formatted as bed files, and sorted by chromosome and start columns. The bed files are stored in a directory indicating release and genome assembly. Any bed file in the release/assembly directory will be displayed as available annotation. You can choose desired annotations by selecting the overlap and/or neighbor option. By default, only the first overlapping annotation is reported. Select the 'report multiple overlaps' option to see all overlapping annotations.

The regions to be annotated can be supplied as directly pasted text, uploaded from a text file, or read from a URL pointing to a bed file. When submitting a file or a URL upload, you will be automatically returned to the input text area with the content of those files being displayed. To start annotation, click the Submit button. You can use example regions for testing purposes by clicking the example buttons. The input regions you supply in the Annotate page will be remembered also in the Custom or the Distance page. This means that you can annotate your regions consecutively with provided or custom annotations without the need to re-submit your regions.

The annotation results are displayed in a table that can be filtered for terms of interest. All annotations are displayed in a single column. You may want to download the annotation results and paste them into an Excel table where each annotation will be displayed in a separate column. Your result files will be deleted after two hours.

Quick tutorial