Testing whether a set of code words satisfies a given set of constraints

Hsin Wen Wei*, Wan Chen Lu, Pei Chi Huang, Wei Kuan Shih, Ming-Yang Kao

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

This paper investigates the problem of testing whether a set of code words satisfies certain biologically motivated Hamming distance constraints. The paper provides three efficient techniques to verify the code words, namely, the Enumeration, Table Lookup, and Encoding methods, with applications to the design of DNA words. The Enumeration method enumerates all combinations of positions in a word, so that all the words in a set can be compared simultaneously and the testing process is improved. The Table Lookup method constructs a data table and divide each word into sub-words to reduce the time complexity of the testing process. The Encoding method which is similar to Table Lookup method uses a linked list to store necessary information in addition. The proposed methods run in O(n) - O(log log n) times faster than the naive method when l = O(log n), where n is the number of code words in a set and l is the length of a word.

Original languageEnglish (US)
Pages (from-to)333-346
Number of pages14
JournalJournal of Information Science and Engineering
Volume26
Issue number2
StatePublished - Mar 1 2010

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Keywords

  • Code word verification
  • Distance constraint
  • Dna verification
  • Dna word design
  • Testing algorithm

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Hardware and Architecture
  • Library and Information Sciences
  • Computational Theory and Mathematics

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