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Advances in Bioinformatics
Volume 2010, Article ID 708501, 12 pages
Research Article

Designing Efficient Spaced Seeds for SOLiD Read Mapping

1INRIA Lille-Nord Europe, LIFL/CNRS, Université Lille 1, 59655 Villeneuve d'Ascq, France
2J.-V.Poncelet Laboratory, Bolshoy Vlasyevsky 11, Moscow 119002, Russia

Received 17 November 2009; Revised 28 March 2010; Accepted 5 July 2010

Academic Editor: Siu-Ming Yiu

Copyright © 2010 Laurent Noé et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.