Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Hardware aspects of algorithm generation

Bezier splines can be used to define the outlines of attractive fonts for high resolution laser printers. Pratt (1985) has shown how Pitteway’s conic drawing algorithm can be constrained to work with integers only, with the control of start and end points necessary to avoid bleeding from the seedfill of the outlines. Modern display devices cannot match the resolution of the printers, but many offer a grey-scale capability which can be used to improve the appearance of the edges bewteen lit and unlit regions. The conic drawing algorithm can be adapted for this purpose, while retaining integer control