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A Comprehensive Review on Protein Sequence Analysis Techniques

P. Haritha1 , P. Shanmugavadivu2 , S. Dhamodharan3

Section:Review Paper, Product Type: Journal Paper
Volume-6 , Issue-7 , Page no. 1433-1442, Jul-2018

CrossRef-DOI:   https://doi.org/10.26438/ijcse/v6i7.14331442

Online published on Jul 31, 2018

Copyright © P. Haritha, P. Shanmugavadivu, S. Dhamodharan . 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.

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IEEE Style Citation: P. Haritha, P. Shanmugavadivu, S. Dhamodharan, “A Comprehensive Review on Protein Sequence Analysis Techniques,” International Journal of Computer Sciences and Engineering, Vol.6, Issue.7, pp.1433-1442, 2018.

MLA Style Citation: P. Haritha, P. Shanmugavadivu, S. Dhamodharan "A Comprehensive Review on Protein Sequence Analysis Techniques." International Journal of Computer Sciences and Engineering 6.7 (2018): 1433-1442.

APA Style Citation: P. Haritha, P. Shanmugavadivu, S. Dhamodharan, (2018). A Comprehensive Review on Protein Sequence Analysis Techniques. International Journal of Computer Sciences and Engineering, 6(7), 1433-1442.

BibTex Style Citation:
@article{Haritha_2018,
author = {P. Haritha, P. Shanmugavadivu, S. Dhamodharan},
title = {A Comprehensive Review on Protein Sequence Analysis Techniques},
journal = {International Journal of Computer Sciences and Engineering},
issue_date = {7 2018},
volume = {6},
Issue = {7},
month = {7},
year = {2018},
issn = {2347-2693},
pages = {1433-1442},
url = {https://www.ijcseonline.org/full_paper_view.php?paper_id=2623},
doi = {https://doi.org/10.26438/ijcse/v6i7.14331442}
publisher = {IJCSE, Indore, INDIA},
}

RIS Style Citation:
TY - JOUR
DO = {https://doi.org/10.26438/ijcse/v6i7.14331442}
UR - https://www.ijcseonline.org/full_paper_view.php?paper_id=2623
TI - A Comprehensive Review on Protein Sequence Analysis Techniques
T2 - International Journal of Computer Sciences and Engineering
AU - P. Haritha, P. Shanmugavadivu, S. Dhamodharan
PY - 2018
DA - 2018/07/31
PB - IJCSE, Indore, INDIA
SP - 1433-1442
IS - 7
VL - 6
SN - 2347-2693
ER -

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Abstract

Sequence analysis aims to explorethe pattern of DNA, RNA and Protein sequences. This analysis involves sequence alignment and extracts the patterns in sequences for the purpose of classification. Sequence analysis can be performed in several ways such as comparison of sequences, computation of similarity measure and mutation detection, based the degree of conserved sequences. It is useful to perform evolutionary analysis, prediction of gene/protein structures and reconstruction of DNA sequences. Sequence alignment plays a vital role in finding similarities among multiple sequences. This article gives an account on the familiar protein sequences alignment techniques being reported. Sequence alignments are of three types: Pair-wise Alignment, Multiple Sequence Alignment and Structural Alignment. The scope of this survey limits to the first two types of alignment. Pair-wise alignment handles a maximum of two sequences at a time, whereas multiple sequence alignment handles more than two sequences. This paper gives a synoptic view on the mechanisms, merits and demerits of select pairwise alignments and multiple sequence alignment techniques to find similarities among sequences

Key-Words / Index Term

Protein Sequence, Protein Alignment, Local Alignment, Global Alignment, Multiple Sequence Alignment.

References

[1] M. Lehman, “Experiments with Algorithms for DNA Sequence alignment”, Computer Science, Simpson College, Indianola, Iowa 50125, pp.1-14, 2005.

[2] D. Fenstermacher, “Introduction to Bioinformatics”, Journal of American Society for information Science and Technology, Vol.56, pp.440-446, 2005.

[3] B. Alberts, A. Johnson, J. Lewis, “From DNA to RNA”, Molecular Biology”, 4th Edition, 2002.

[4] J. Wu, J. Xiao, Z. Zhang, X. Wang, S. Hu, J. Yu,“Ribogenomics: The Science and Knowledge of RNA”, Genomics Proteomics
Bioinformatics, Vol.22, pp. 57-63, 2014.
[5]R. Chen, H. Yan, K.N. Zhao, B. Martinac, G.B. LIU, “Comprehensive Analysis of Prokaryotic Mechanosensation Genes: Their Characteristics in Codon Usage”, DNA Sequence, pp. 1-10, 2006.

[6] G. Bertram, S. Innes, O. Minella, J. P. Richardson, L. Stansfield, “Endless Possibilities: Translation Termination and Stop Codon Recognition”, Microbiology, Vol.147, pp.255-269, 2001.

[7] T.J.J. Kelly, A.D. Lindeman, S.M. Bridges, “Exploratory visual analysis of conserved domains on multiple sequence alignments”, BMC Bioinformatics, Vol.10,pp. 1-18, 2009.

[8] B.H.A. Rehm, “Bioinformatic Tool for DNA/ Protein Sequence Analysis, Functional Assignment of Genes and Protein Classification”, Applied Microbiology Biotechnology, Vol.57, pp.579-592. 2001.
[9] C.B. Do and K. Katoh, “Protein Multiple Sequence Alignment”, Methods in Molecular Biology, Vol.484, pp. 379-413, 2009.

[10] S. Batzoglou, “The Many Faces of Sequence Alignment”, Briefings in Bioinformatics, Vol.6, pp. 6-22, 2005.
[11] L. Mullan, “Pairwise Sequence alignment”, Briefings in Bioinformatics, Vol. 7, pp. 113-115, 2006.
[12] P. Manohar, S. Singh, “Protein Sequence Alignment: A Review”, World Applied Programming, Vol. 2, pp.141-145, 2012.

[13] Z.M. Zhou, Z.W. Chen, “Dynamic Programming for Protein Sequence Alignment”, International Journal of Bio-Science and Technology, Vol.5, pp. 141-150, 2013.

[14] R. Mott, “Smith-Waterman Algorithm” University of Oxford, DOI: 10.1038/npg.els.0005263, pp. 1-5, 2005.
[15] E.S. Donkor, N.T.K.D. Dayie, T.K. Adiku, “Bioinformatics With Basic Local Alignment Search Tool (BLAST) and Fast Alignment (FASTA)”, Journal of Bioinformatics and Sequence Analysis, Vol. 6, pp.1-6, 2014.
[16] T. Madden, “The BLAST Sequence Analysis Tool”, National Center for Biotechnology Information, pp.1-10, 2013.
[17] T.A. Tatusova, T.L. Madden, “BLAST2 Sequences, a New Tool For Comparing Protein And Nucleotide Sequences”, FEMS Microbiology Letters, Vol. 174, pp. 1-6, 2006.

[18] N.A.A. Rashid, R. Abdullah, A.Z.H.Talib, Z.Ali, “Fast Dynamic Programming Based Sequence Alignment”, IEEE Transactions, pp.1-7,2006.

[19] S.R. Harris, K. Chinyere, Okoro, “New Approaches to Prokaryotic Systematics”, Methods in Microbiology, 2014.
[20] K. Benkrid, Y.Liu, A. Benkrid, “A Highly Parametrized and Efficient FPGA-Based Skeleton for Pair-wise Biological Sequence Alignment”, IEEE Transactions on very large scale integration (VLSI) Systems, Vol. 17,pp. 561-570, 2009.
[21] N. Bray, I. Dubchak, L. Pachter, “AVID: A Global Alignment Program”, Genome Research, Vol. 13, pp. 97-102, 2003.
[22] M. Brudno, C. B. Do, G, M, Cooper, “LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA”, Genome Research, pp. 721-731, 2015.