Optimal Spaced Seeds for Homologous Coding Regions

  title={Optimal Spaced Seeds for Homologous Coding Regions},
  author={Brona Brejov{\'a} and Daniel G. Brown and Tom{\'a}s Vinar},
  journal={Journal of bioinformatics and computational biology},
  volume={1 4},
Optimal spaced seeds were developed as a method to increase sensitivity of local alignment programs similar to BLASTN. Such seeds have been used before in the program PatternHunter, and have given improved sensitivity and running time relative to BLASTN in genome-genome comparison. We study the problem of computing optimal spaced seeds for detecting homologous coding regions in unannotated genomic sequences. By using well-chosen seeds, we are able to improve the sensitivity of coding sequence… CONTINUE READING
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