### 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 language | English (US) |
---|---|

Pages (from-to) | 333-346 |

Number of pages | 14 |

Journal | Journal of Information Science and Engineering |

Volume | 26 |

Issue number | 2 |

State | Published - Mar 1 2010 |

### Fingerprint

### 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

### Cite this

*Journal of Information Science and Engineering*,

*26*(2), 333-346.

}

*Journal of Information Science and Engineering*, vol. 26, no. 2, pp. 333-346.

**Testing whether a set of code words satisfies a given set of constraints.** / Wei, Hsin Wen; Lu, Wan Chen; Huang, Pei Chi; Shih, Wei Kuan; Kao, Ming-Yang.

Research output: Contribution to journal › Article

TY - JOUR

T1 - Testing whether a set of code words satisfies a given set of constraints

AU - Wei, Hsin Wen

AU - Lu, Wan Chen

AU - Huang, Pei Chi

AU - Shih, Wei Kuan

AU - Kao, Ming-Yang

PY - 2010/3/1

Y1 - 2010/3/1

N2 - 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.

AB - 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.

KW - Code word verification

KW - Distance constraint

KW - Dna verification

KW - Dna word design

KW - Testing algorithm

UR - http://www.scopus.com/inward/record.url?scp=77950405104&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77950405104&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:77950405104

VL - 26

SP - 333

EP - 346

JO - Journal of Information Science and Engineering

JF - Journal of Information Science and Engineering

SN - 1016-2364

IS - 2

ER -