Designing Efficient Spaced Seeds for SOLiD Read Mapping. - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Advances in Bioinformatics Year : 2010

Designing Efficient Spaced Seeds for SOLiD Read Mapping.

Abstract

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.

Dates and versions

inria-00527029 , version 1 (17-10-2010)

Identifiers

Cite

Laurent Noé, Marta Gîrdea, Gregory Kucherov. Designing Efficient Spaced Seeds for SOLiD Read Mapping.. Advances in Bioinformatics, 2010, ⟨10.1155/2010/708501⟩. ⟨inria-00527029⟩
91 View
0 Download

Altmetric

Share

Gmail Facebook X LinkedIn More