Efficient algorithms for searching for exact repetition of nucleotide sequences

Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


There are several algorithms designed for searches for homologous sequences (Fitch 1966; Needleman and Wunsch 1970; Chva'tal and Sankoff 1975; Griggs 1977; Sannkoff 1972; Smith and Waterman 1981; Smith et al. 1981, Wagner and Fisher 1974; Waterman et al. 1976). This paper presents some very simple and useful high speed, "text editing" algorithms that search for exact nucleotide sequence repetition and genome duplication. The last algorithm suggested here is specifically adapted for the 4-letter alphabet of nucleotide sequences. Owing to the rapid accumulation of nucleotide sequences and the frequent need to search for sequence repetition or where a given set of nucleotides occurs in long sequences, efficient algorithms of this type are a necessity.

Original languageEnglish
Pages (from-to)283-285
Number of pages3
JournalJournal of Molecular Evolution
Issue number3-4
StatePublished - Jul 1983
Externally publishedYes


  • Algorithm
  • Exact repetition
  • Sequence analysis


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