DNA physical mapping on a reconfigurable platform

Abstract

Reconfigurable architectures enable the hardware function to be implemented by the user and, due to its characteristics, have been used in many areas, including Bioinformatics. One application of Bioinformatics is the consecutive ones problem, which consists in finding a permutation of columns in a binary matrix, in such a way that all the ones in each row are consecutive. This matrix represents information about DNA fragments and probes, which allow the determination of the order of the nitrogenated bases that form the original DNA. This work proposes a hybrid software/hardware system for solving the consecutive ones problem. Since this problem processes large volumes of data, the goal is to reduce its execution time, compared to a SW algorithm. We present and analyze several implementations, in the reconfigurable hardware, of sections of this algorithm, using a Virtex-II FPGA. Experiments performed using real chromosomes produced speedups of up to 29.62 and show potential for further optimizations exploiting dynamic reconfiguration. © 2008 Springer-Verlag Berlin Heidelberg.