REDUCING THE SEARCH SPACE AND TIME COMPLEXITY OF NEEDLEMAN-WUNSCH ALGORITHM (GLOBAL ALIGNMENT) AND SMITH-WATERMAN ALGORITHM (LOCAL ALIGNMENT) FOR DNA SEQUENCE ALIGNMENT

Authors

  • F. N. Muhamad School of Computer & Communication Engineering, Universiti Malaysia Perlis, Perlis, Malaysia
  • R. B. Ahmad School of Computer & Communication Engineering, Universiti Malaysia Perlis, Perlis, Malaysia
  • S. Mohd. Asi School of Computer & Communication Engineering, Universiti Malaysia Perlis, Perlis, Malaysia
  • M. N. Murad School of Manufacturing Engineering, Universiti Malaysia Perlis, Perlis, Malaysia

DOI:

https://doi.org/10.11113/jt.v77.6564

Keywords:

Sequence comparison, sequence alignment, global alignment, local alignment, similarity, optimal alignment, scoring, traceback, match, mismatch, gaps

Abstract

The fundamental procedure of analyzing sequence content is sequence comparison. Sequence comparison can be defined as the problem of finding which parts of the sequences are similar and which parts are different, namely comparing two sequences to identify similarities and differences between them. A typical approach to solve this problem is to find a good and reasonable alignment between the two sequences. The main research in this project is to align the DNA sequences by using the Needleman-Wunsch algorithm for global alignment and Smith-Waterman algorithm for local alignment based on the Dynamic Programming algorithm. The Dynamic Programming Algorithm is guaranteed to find optimal alignment by exploring all possible alignments and choosing the best through the scoring and traceback techniques. The algorithms proposed and evaluated are to reduce the gaps in aligning sequences as well as the length of the sequences aligned without compromising the quality or correctness of results. In order to verify the accuracy and consistency of measurements obtained in Needleman-Wunsch and Smith-Waterman algorithms the data is compared with Emboss (global) and Emboss (local) with 600 strands test data.

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Published

2015-12-01

How to Cite

Muhamad, F. N., Ahmad, R. B., Mohd. Asi, S., & Murad, M. N. (2015). REDUCING THE SEARCH SPACE AND TIME COMPLEXITY OF NEEDLEMAN-WUNSCH ALGORITHM (GLOBAL ALIGNMENT) AND SMITH-WATERMAN ALGORITHM (LOCAL ALIGNMENT) FOR DNA SEQUENCE ALIGNMENT. Jurnal Teknologi, 77(20). https://doi.org/10.11113/jt.v77.6564