  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.
