Effective cluster-based seed design for cross-species sequence comparisons

Leming Zhou, Ingrid Mihai, Liliana Florea

Research output: Contribution to journalArticlepeer-review


To annotate newly sequenced organisms, cross-species sequence comparison algorithms can be applied to align gene sequences to the genome of a related species. To improve the accuracy of alignment, spaced seeds must be optimized for each comparison. As the number and diversity of genomes increase, an efficient alternative is to cluster pairwise comparisons into groups and identify seeds for groups instead of individual comparisons. Here we investigate a measure of comparison closeness and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed.

Original languageEnglish (US)
Pages (from-to)2926-2927
Number of pages2
Issue number24
StatePublished - Dec 2008
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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