Improved approximate common interval

Amihood Amir, Leszek Gasieniec, Riva Shalom

Research output: Contribution to journalArticle

12 Scopus citations

Abstract

The approximate common interval (ACI) problem, where the multiple genome strings are required to be compared to all other character sets of the other string is discussed. Genomes are considered as strings, with possible repeats of symbols representing paralogous genes, and detect the gene clusters by modeling gene intervals by the set of characters. A specific number of time algorithm that locates all intervals of two strings share the same character set, which also represents the number of the strings. This approximate common interval (ACI) problem for a specific number of strings can be solved in time and space by considering a finite length of every string. A procedure for extracting all maximal character sets of the input strings, and the ACI problem for a single input string and multiple input strings are studied. Graphic representation shows provides a simple and versatile algorithm, supporting the approximate common interval problem.

Original languageEnglish (US)
Pages (from-to)142-149
Number of pages8
JournalInformation Processing Letters
Volume103
Issue number4
DOIs
StatePublished - Aug 16 2007
Externally publishedYes

Keywords

  • Computational biology
  • Design of algorithms
  • Gene evolution
  • Hamming distance
  • Pattern matching

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Signal Processing
  • Information Systems
  • Computer Science Applications

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