doi: 10.7763/IJFCC.2015.V4.377
Efficient Sequence Comparison Using Binary Codes
Hossein Kamel Rahimi
- Faculty of Science and Engineering, Queensland University of Technology, Australia.
Abstract
In this paper, we propose an efficient way of finding the exact distance in sequence comparison by using Huffman coding method for alphabets with uniform symbol probabilities. The approach is proposed as a refinement for word pair comparison in D2 statistics, though it can readily be generalised. Two given sequences with identical lengths are encoded to Huffman binary codes by which we are able to calculate Hamming Distance using binary operations efficiently. This method is applied on D2 statistics to compare <em>k-tuples</em> faster than its original version. The evaluation on emprical sequences showed that the method is faster than original D2; especially, when re-using the encoded sequences which resulted in better performance.
Keywords
- Performance
- experimentation
- string and sequence processing
- huffman encoding
- hamming distance
- D2 statistics
- string comparison
- binary codes
- bitwise operation
How to Cite
Hossein Kamel Rahimi, "Efficient Sequence Comparison Using Binary Codes," International Journal of Future Computer and Communication, vol. 4, no. 3, pp. 165-169, 2015. https://doi.org/ 10.7763/IJFCC.2015.V4.377
Copyright & License
Copyright © 2015 by the authors. This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).