  Recent technological advances in Next Generation Sequencing tools have led to
increasing speeds of DNA sample collection, preparation, and sequencing. One
instrument can produce over 600 Gb of genetic sequence data in a single run.
This creates new opportunities to efficiently handle the increasing workload.
We propose a new method of fast genetic sequence analysis using the Dynamic
Distributed Dimensional Data Model (D4M) - an associative array environment for
MATLAB developed at MIT Lincoln Laboratory. Based on mathematical and
statistical properties, the method leverages big data techniques and the
implementation of an Apache Acculumo database to accelerate computations
one-hundred fold over other methods. Comparisons of the D4M method with the
current gold-standard for sequence analysis, BLAST, show the two are comparable
in the alignments they find. This paper will present an overview of the D4M
genetic sequence algorithm and statistical comparisons with BLAST.
