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hyphaltip edited this page Sep 13, 2010
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ShortReadDB is for managing fast mapping of genomic locations (short reads) against genomic features (annotations, genes, etc) in SQL. It uses GIS functions for finding genome coordinate overlaps. There is a mysql and postgres implementation, but the mysql implementation is stalled as it was significantly slower than the postgres in my experience. The Postgresql implementation uses PostGIS implementation for location overlap calculations.