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arXiv · 1805.08816

copMEM: Finding maximal exact matches via sampling both genomes

Szymon Grabowski·Wojciech Bieniecki
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Abstract

Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in parallel regimes, is not quite satisfactory. We present a new algorithm, copMEM, that allows to sparsely sample both input genomes, with sampling steps being coprime. Despite being a single-threaded implementation, copMEM computes all MEMs of minimum length 100 between the human and mouse genomes in less than 2 minutes, using less than 10 GB of RAM memory.

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Szymon Grabowski, Wojciech Bieniecki. 2018-05-22. copMEM: Finding maximal exact matches via sampling both genomes. https://arxiv.org/abs/1805.08816

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