Algorithms for mapping short degenerate and weighted sequences to a reference genome

Abstract

Novel high-throughput (Deep) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of short sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design algorithms for Massive Exact and Approximate Pattern Matching of short degenerate and weighted sequences, derived from Deep sequencing technologies, to a reference genome.

Parallel Algorithms for Mapping Short Degenerate and Weighted Dna Sequences to a Reference Genome

“…The sequential versions of Algorithm I and Algorithm II were implemented on a real dataset and presented in [6] and [9], giving some very promising results comparing to more traditional approaches. Our immediate target is to build a software tool, which will be based on the presented algorithms, and will be used by the biologists for mapping short sequences to a reference genome.…”

“…In this paper, we design parallel algorithms for addressing the problem of efficiently mapping millions of short degenerate and weighted DNA sequences to a reference genome. The proposed parallel algorithms make use of the messagepassing paradigm, and resemble the sequential strategies presented in [6] and [9]. Our approach distributes the genomic sequence among the available processors, and preprocesses it, by using word-level parallelism and parallel sorting.…”

Longest Common Subsequence on Weighted Sequences

“…Other interesting results include approximate and gapped pattern matching [5,28], property matching [2], swapped matching [27], the all-covers and all-seeds problem [26,29], and extracting motifs [20]. There are also some more practical results on mapping short weighted sequences to a reference genome [6], a problem that has also been studied in the parallel setting [19], as well as on the reporting version of the problem which we also consider in this paper [9].…”