Communications in Information and Systems

Volume 10 (2010)

Number 2

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

Pages: 115 – 136



Liliana Florea

Ingrid Mihai

Leming Zhou


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.


cDNA; genome; spaced seeds; Markov model

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