Designing Efficient Spaced Seeds for SOLiD Read Mapping

Laurent Noé, Marta Gîrdea, Gregory Kucherov
2010 Advances in Bioinformatics  
The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome. The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping. Our method can handle both
more » ... ssy and lossless frameworks and is able to distinguish, at the level of seed design, between SNPs and reading errors. We illustrate our approach by several seed designs and demonstrate their efficiency.
doi:10.1155/2010/708501 pmid:20936175 pmcid:PMC2945724 fatcat:nahdomgtm5bfpf3pk2mrmifh2i