Local Alignments of DNA Sequences with the Connex Array

This paper presents a heuristic for finding close to optimal solutions to the local alignment problem of two DNA sequences, and more precisely to the gene prediction problem on the Connex Array circuit, a new hierarchical parallel in-memory device. Though not optimal, the solutions generated by our algorithm compare well with those generated by other algorithms in the public domain. When aligning a probe of N symbols to a target of M symbols, the algorithm has a theoretical time complexity of O(N log(N)), with a small constant of proportionality, and requires no preprocessing of the data. However, experimental results exhibit quasi-linear time complexity.