Genomedata

December 22, 2009 8:18 PM

Genomedata
Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. We have also developed utilities to load data into this format. A reference implementation in Python and C components is available here under the GNU General Public License.
posted by grouse (4 comments total)

For those of us who don't work with genomes ourselves: what sort of projects is this application useful for?
posted by ocherdraco at 8:22 AM on December 23, 2009

You can think of the human genome sequence like a base map, and this system allows you to easily add layers on top of that map, much as you would add terrain, temperature, air pressure, or radar layers on top of a base map of the shape of the U.S.

There are experiments that will tell you every genomic location where a particular protein is likely to be found—the protein itself, not the DNA encoding its gene. I use this software to add a layer for each protein that tells how likely it is that a protein is at a particular location. I've been developing software that finds patterns in this sort of data, which will probably be a future submission to MeFi Projects.
posted by grouse at 8:48 AM on December 23, 2009

Cool!
posted by ocherdraco at 8:54 AM on December 23, 2009

An application note on Genomedata has now been accepted to the peer-reviewed journal Bioinformatics.
posted by grouse at 10:10 AM on May 5, 2010