An efficient code searching for sequence homology and DNA duplication

Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


This paper presents a very simple and efficient algorithm that searches for sequence homology and gene duplication. The code finds the best alignment of two, short or long, sequences without having to specify how many unmatched bases are allowed to be looped out. Following Needleman & Wunsch 1970, Seller 1974 Sankoff 1972 and Smith, Waterman & Fitch 1981 gap constraints are incorporated into the program and may be employed. The availability of such a fast computer code enables detection of homologous genes which may fulfill a different function at present, but have arisen from a common gene-ancestor. The code is extremely fast and runs in O(n 3 2) units of time. It was applied to the θX174 sequence.

Original languageEnglish
Pages (from-to)319-328
Number of pages10
JournalJournal of Theoretical Biology
Issue number2
StatePublished - 21 Jan 1983
Externally publishedYes


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