Spaced Seeds for Cross-species CDNA-to-genome Sequence Alignment

We review recent developments in spaced seed design for cross-species sequence alignment. We start with a brief overview of original ideas and early techniques, and then focus on more recent work on finding accurate (sensitive and specific) seeds for cross-species cDNA-to-genome alignment. These recent developments include methods and models for estimating seed specificity and determining sensitive and specific seeds, finding seeds that can be applied to a wide range of comparisons, and applying seed models to other computational biology areas, such as gene finding.

Keywords

cDNA, genome, spaced seeds, Markov model

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Published 1 January 2010