AnnotateGenomicRegions Files

AnnotateGenomicRegions is web application for annotating genomic regions.

Running AnnotateGenomicRegions requires an installation of the Glassfish web server 
(version 3 has been used for testing, but other versions may work as well) 
and deploying this web archive (AnnotateGenomicRegions.war) on Glassfish.

The application shall respond to this URL:

http://yourDomain:yourPort/AnnotateGenomicRegions/index.html

This distribution of AnnotateGenomicRegions comes with annotations for hg19 and mm9. 
New annotations and genomes can be added by creating a folder with the genome name
in the root directory of the application and adding the desired annotations in a 
tab-separated text file in the format

chr	start1	end1	annotationString1
chr	start2	end2	annotationString2
etc

The application will list newly added genomes and annotations automatically when the 
"ANNOTATE" menu option is clicked. Using the "ANNOTATE" menu option provides access to
server-side annotations of frequent use.

Since not each and every annotation can be hosted on the server, there is a custom annotation
option available under "CUSTOM", where users can upload their own annotations along with the
genomic regions to annotate. Specifying the number of desired custom annotations will display
the necessary number of browse buttons for upload.
Since both the annotations and the genomic regions need to travel
over the web, large annotation files with more than 100000 entries should be avoided. 

Both the "ANNOTATE" and the "CUSTOM" option ignore strand information and return overlapping 
and/or neighboring genome annotations. 

For calculating distances between genomic regions and genome annotations, strand information is required.
Therefore, in the "DISTANCE" option, which works in a similar fashion like the custom option, 
users can upload custom annotations with strand information and specify whether they want the distance to be calculated
to the 5'end, the 3'end, the start, the end, or the center position of the genome annotation. 
Here, 5'end is identical to the start position for annotations on the + strand 
and 3'end is identical to the end position for annotations on the - strand. 
The start position is always smaller than the end position, regardless of strandedness.

For bug reports, please contact heiko.muller@ifom-ieo-campus.it