Abstract
With the massive amount of biological sequence data being generated by current technologies there is an urgent need to come out with faster sequence comparison methods. Most of the existing sequence comparison methods are alignment based which are proven to be very computationally complex when compared to the alignment free methods. In this paper, we have proposed alignment free methods for analysis of promoter sequences. Promoter sequences play a crucial role in gene regulation. After extracting the promoter sequence, matrices of motif frequency with position information (Position Specific Motif Matrix (PSMM)) is constructed, this is further taken for promoter analysis. These designed Frequency Based (FD) algorithms are tested on three different promoter datasets obtained from NCBI and UCSC repositories. The results show high similarity values for promoters with similar functionality and low values otherwise.
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References
Qui, P.: Recent Advances in Computational Promoter Analysis in Understanding the Transcriptional Regulatory Network. Biochem. Biophys. Res. Commun. 309(3), 495–501 (2003)
Ohler, U., Niemann, H.: Identification and Analysis of Eukaryotic Promoters: Recent Computational Approaches. Trends Genet. 17(2), 56–60 (2001)
Chowdhary, R., Lam Tan, S., Ali, R.A., Boerlage, B., Wong, L., Bajic, B.V.: Dragon Promoter Mapper (DPM): A Bayesian Framework for Modelling Promoter Structures. Bioinformatics 22(18), 2310–2312 (2006)
Felsenstein, J.: Inferring Phylogenies. Am. J. Hum. Genet. 74(5), 1074 (2004)
Penner, O., Grassberger, P., Paczuski, M.: Sequence Alignment, Mutual Information, and Dissimilarity Measures for Constructing Phylogenies. PLoS One 6(1) (2011)
Edgar, R.C.: MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput. Nucleic Acids Res. 32(5), 1792–1797 (2004)
Blaisdell, B.E.: A Measure of Similarity of Sets of Sequences not Requiring Sequence Alignment. Proc. Natl. Acad. Sci. 83(14), 5155–5159 (1986)
Soares, I., Goios, A., Amorim, A.: Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency. The Scientific World Journal 2012Â (2012)
Leimeister, C.A., Boden, M., Horwege, S., Linder, S., Morgenstern, B.: Fast Alignment-Free Sequence Comparison Using Spaced-Word Frequencies. Bioinformatics 30(14), 1991–1999 (2014)
Luo, J., Li, R., Zeng, Q.: A Novel Method for Sequence Similarity Analysis Based on the Relative Frequency of Dual Nucleotides. MATCH Commun. Math. Comput. Chem. 59, 653–659 (2008)
Mantaci, S., Restivo, A., Sciortino, M.: Distance Measures for Biological Sequences: Some Recent Approaches. Internat. J. Approx. Reason. 47, 109–124 (2008)
Vinga, S., Almeida, J.: Alignment-Free Sequence Comparison-A Review. Bioinformatics 19(4), 513–523 (2003)
Blaisdell, B.E.: Effectiveness of Measures Requiring and not Requiring Prior Sequence Alignment for Estimating the Dissimilarities of natural Sequences. J. Mol. Evol. 29, 526–537 (1989)
Hu, J., Liang, X., Zhao, H., Chen, D.: The Analysis of Similarity for Promoter Sequence Structures in Yeast Genes. In: 5th BMEI, pp. 919–922 (2012)
Meera, A., Kouser, R.L.: Comparison of Promoter Sequences Based on Inter-Motif Distance. IJSSCI 3(3), 57–68 (2011)
Meera, A., Kouser, R.L., Bhat, S.: Computational Approach Towards Finding Evolutionary Distance and Gene Order Using Promoter Sequences of Central Metabolic Pathway. Interdiscip. Sci. 3(1), 43–49 (2011)
Kouser, R.L.: Similarity Analysis of Position Specific Motif Matrices using Lacunarity for Promoter Sequences. In: ICONIAAC 2014, Article. 37. ACM, New York (2014)
Meera, A., Kouser, R.L., Shilpa, N.: New distance Measure for Sequence Comaprison Using Cumulative Frequency Distribution. IJCA 19(2), 13–18 (2011)
Huang, A.C., Hu, L., Kauffman, S.A., Zhang, W., Shmulevich, I.: Using Cell Fate Attractors to Uncover Transcriptional Regulation of HL60 Neutrophil Differentiation. BMC Syst. Biol. 20(3) (2009)
Levenshtein, V.I.: Binary Codes Capable of Correcting Deletions, Insertions, and Reversals. Cybern. Control Theory 10(8), 707–710 (1966)
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Kouser, Rangarajan, L., Chandrashekar, D.S., Kshitish, K.A., Abraham, E.M. (2015). Alignment Free Frequency Based Distance Measures for Promoter Sequence Comparison. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9044. Springer, Cham. https://doi.org/10.1007/978-3-319-16480-9_19
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DOI: https://doi.org/10.1007/978-3-319-16480-9_19
Publisher Name: Springer, Cham
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