Designing Efficient Spaced Seeds for SOLiD Read Mapping
Copyright policy )Designing Efficient Spaced Seeds for SOLiD Read Mapping
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 lossy 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.
Spaced seeds, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Applied Biosystems SOLiD, read mapping, Biochemistry, molecular biology, ACM: E.: Data/E.2: DATA STORAGE REPRESENTATIONS/E.2.2: Hash-table representations, 005, ACM: G.: Mathematics of Computing/G.4: MATHEMATICAL SOFTWARE/G.4.4: Parallel and vector implementations, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.3: Applications, seed design, color space alignment, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics and epigenetics, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Research Article
Spaced seeds, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Applied Biosystems SOLiD, read mapping, Biochemistry, molecular biology, ACM: E.: Data/E.2: DATA STORAGE REPRESENTATIONS/E.2.2: Hash-table representations, 005, ACM: G.: Mathematics of Computing/G.4: MATHEMATICAL SOFTWARE/G.4.4: Parallel and vector implementations, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.3: Applications, seed design, color space alignment, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics and epigenetics, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Research Article
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