DNA Sequence Alignment Engine: An AM-based design

Lowering the time and cost of performing pairwise sequence alignment (PSA) on large and exponentially growing DNA Databases poses a big research challenge. Neither the current practice of running the complex programs on highly expensive parallel or networked computers nor the relatively recent proposals for implementing the algorithms on high-speed general-purpose hardware platforms by heavily relying on specialized software can provide the desired cost-time performance. A novel special-purpose hardware system named DNA Sequence Alignment Engine (DSAE) which is based on an associative memory (AM) built with a large collection of content-to-address memory (CTAM) modules has been described. Time-staggered parallelism of the CTAM modules and their independent binary search of deep segments of the DNA database promises highly scalable and very high-speed sequence alignment at a relatively low-cost. Only ungapped alignment has been studied so far in this ongoing research.