Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species and in identifying conserved genes. In this paper, we present a parallel algorithm for computing syntenic alignments that runs in [Formula: see text] time, where m and n are the respective lengths of the two genomic sequences, and p is the number of processors used. Our algorithm is time optimal with respect to the corresponding sequential algorithm and can use [Formula: see text] processors, where n is the length of the larger sequence. The space requirement of the algorithm is [Formula: see text] per processor. Using an implementation of this parallel algorithm, we report the alignment of a gene-rich region of human chromosome 12, namely 12p13 and its syntenic region in mouse chromosome 6 (both over 220,000 base pairs in length) in under 24 minutes on a 64-processor IBM xSeries cluster.
DNA sequences alignment in multi-GPUs: acceleration and energy payoff
