Compressive genomics for protein databases

Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger

Abstract: : The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly as fast; we can exploit this fact to greatly accelerate homology search. Acceleration of programs in the popular PSI/DELTA-BLAST family of tools will not only speed-up homology search directly but also the huge collection of other current programs that primarily interact with large protein databases via precisely these tools.