New algorithms for the spaced seeds

Xin Gao, Shuai Cheng Li, Yinan Lu*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations


The best known algorithm computes the sensitivity of a given spaced seed on a random region with running time O((M+L)|B|), where M is the length of the seed, L is the length of the random region, and |B| is the size of seed-compatible-suffix set, which is exponential to the number of 0's in the seed. We developed two algorithms to improve this running time: the first one improves the running time to O(|B′|2ML), where B′ is a subset of B; the second one improves the running time to O((M|B|) 2.236log(L/M)), which will be much smaller than the original running time when L is large. We also developed a Monte Carlo algorithm which can guarantee to quickly find a near optimal seed with high probability.

Original languageEnglish (US)
Title of host publicationFrontiers in Algorithmics - First Annual International Workshop, FAW 2007, Proceedings
PublisherSpringer Verlag
Number of pages12
ISBN (Print)9783540738138
StatePublished - 2007
Externally publishedYes
Event1st International Frontiers in Algorithmics Workshop, FAW 2007 - Lanzhou, China
Duration: Aug 1 2007Aug 3 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4613 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other1st International Frontiers in Algorithmics Workshop, FAW 2007


  • Bioinformatics
  • Homology search
  • Spaced seed

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


Dive into the research topics of 'New algorithms for the spaced seeds'. Together they form a unique fingerprint.

Cite this