Multiple spaced seeds for homology search

  title={Multiple spaced seeds for homology search},
  author={Lucian Ilie and Silvana Ilie},
  volume={23 22},
MOTIVATION Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. The introduction of optimal spaced seeds in PatternHunter has increased both the sensitivity and the speed of homology search, and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, Smith-Waterman sensitivity is approached at BLASTn speed. However, computing optimal multiple spaced… CONTINUE READING
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