An Improved Needleman-Wunsch Algorithm for Pairwise Sequence Alignment of Protein-Albumin

Lailil Muflikhah, Dian Eka R.


This paper aims to improve the method of optimal global sequence alignment in order to increase the computational performance. The huge number of genome sequences is main problem of alignment. One of global sequence alignment methods is Needleman-Wunsch algorithm. This algorithm is implemented by constructing a MxN matrix, which M is the length of first sequence and N is the length of second sequence. All cells of the matrix are filled to compute the score for constructing global pairwise sequence alignment, so that the time and space complexity are very high. Therefore, the improved Needleman-Wunsch algorithm (INWA) is addressed to compute partially for the score in the cells. The test set consisted of 1250 pairwise sequence alignments of human protein-albumin and it is compared to the original method. As a result shows that the space and time compexity of INWA is O(N) instead of O(MN).


Genome; Needleman-Wunsch; ProteinAlbumin; Sequence Alignment;

Full Text:



Rajaee, N., Ahmad S., Awang, Zulkharnain, A., ‚ÄúComparison between Double Stranded DNA with Restriction Enzymes and Single Stranded DNA with Primers for Solving Boolean Matrix Multiplication‚ÄĚ, Journal of Telecommunication, Electronic and Computer Engineering, vol. 8 no. 12, pp.5-8, 2016.

EMBL-EBI, "Pairwise Sequence Alignment," 2015. [Online]. Available: [Accessed 8 10 2015].

S. Needleman and C. Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two sequences," Journal of Molecular Biology, vol. 48, no. 3, pp. 443-453, 1970.

T. Smith and M. Waterman, "Identification of common molecular subsequences," J. Mol. Biol., vol. 147, pp. 195-197, 1981.

W. Pearson and D. Lipman, "FASTA: Improved tools for biological sequence comparison," in Proceedings of the National Academy of Sciences, USA, 1988.

S. F. Altschul, W. Gish, W. Miller, E. Myers and D. Lipman, "Basic Local Alignment Search Tool," Journal of Molecular Biology, vol. 215, pp. 403-410, 1990.

NCBI, "NCBI," 2015. [Online]. Available: PAGE_TYPE=BlastSearch&LINK_LOC=blasthome. [Accessed 6 May 2015]

Zhou Zm, Chen Z-w. Dynamic Programming for Protein Sequence Alignment. International Journal of Bio-Science and Bio-Technology. 2013; 5(2): 141-150.

Rahmad A., Auriza, Sukoco H., Kusuma, A.W. Comparison of Data Partitioning Schema of Parallel Pairwise Alignment on Shared Memory System. TELKOMNIKA, Telecomunication, Computing, Electronics and Control. 2015; 13(2): 694-702.

. Yamada, Kazunori D, Optimixing Scoring Function of Dynamic Programming of Pairwise Profile Alignment using Derivative Free Network, Graduate School of Information Sciences, Tohoku University Sendai, Japan,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan. arXiv:1708. 09097v2 [q-bio.QM]. September 2017.

S. A.Shehab, A. Keshk and H. Mahgoub, "Fast Dynamic Algorithm for Sequence Alignment based on Bioinformatics," International Journal of Computer Applications, vol. 32, no. 7, pp. 54-61, 2012.

J. Xiong, "Essential Bioinformatics," Cambridge University Press, p. 4. 2006.

N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, S. Istrail, P. Pevzner and M. Waterman, Eds., Massachusetts: The MIT Press, 2004.

H. A. S. A. S. M. F. T. Ahmad M. Hosny, "An Efficient Solution for Aligning Huge DNA Sequences," in ICCES, Cairo, 2011.


  • There are currently no refbacks.

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.

ISSN: 2180-1843

eISSN: 2289-8131