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Alignment Beyond Sequences: Forwards and Backwards in Colors and DAGs

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In this lecture I will present the algorithmic challenges presented by two novel types of sequencing technologies: the SOLiD system, which generates color-space reads, and Single-Molecule Sequencing systems, which have an extremely high indel error rate, but can read each piece of DNA two or more times. I will then explain how classical string alignment algorithms must be adopted to deal with this type of data, in particular explaining the generalization of sequence alignment to the Weighted Sequence Graph abstraction, and showing how this can be further adopted to work with color-space data

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