Enhanced Single Bit DNA Squeezer (ESBDNAS)

Authors

  • Dr. S. Panneer Arokiaraj  Associate Professor, Computer Science, PERIYAR EVR College, Trichy, Tamil Nadu, India
  • Alam Jahaan   Research Scholar, Computer Science, PERIYAR EVR College, Trichy, Tamil Nadu, India

Keywords:

DNA sequence, bit based method, DNA compression, Bit DNA Squeezer, SBDNAS, Bit- based DNA compression

Abstract

DNA Sequences contain concatenation of the four nucleotides or bases namely, Adenine, Guanine, Thymine and Cytosine. These nucleotides form a double stranded helix with each base of one strand joined to its complement on the other strand by using hydrogen bonds through base pairing rules. DNA compression may be carried out by reducing redundancy and exploiting the properties of DNA sequences. This paper proposes ENHANCED SINGLE BIT DNA SQUEEZER (ESBDNAS) an enhanced bit based lossless compression algorithm to compress a DNA sequence which implements two stages and is similar to SBDNAS (Single Bit DNA Squeezer) Algorithm. The proposed method converts the bases to bits 0 or 1 using the BDNAS algorithm and exploits the properties of DNA sequences that are inherent in it by substituting exact repeats, palindromes and their respective reverses for selected sub-sequences. This method achieves a compression ratio that is better than the existing lossless bit based DNA sequence compression algorithms.

References

  1. https://en.wikipedia.org/wiki/DNA
  2. https://en.wikipedia.org/wiki/Introduction_to_genetics
  3. Manzini G. and Raster0 M., "A simple and fast DNA compressor, Software: Practice and Experience", MUIR support projects(ALINWEB), vol. 34(14), pp.1397-1411, 2004
  4. AlamJahaan, Dr T.N. Ravi, "Scrutiny Of Lossless Compression Techniques Using A Few Quality Measures", International Journal Of Advanced Research In Computer Science And Applications Issn 2321- 872x, Volume 4, Issue 3, March 2016.
  5. SR. Kodituwakku Et. Al. "Comparison Of Lossless Data Compression Algorithms For Text Data", Indian Journal Of Computer Science And Engineering, Vol 1 No 4 416-425
  6. https://www.hackerearth.com/practice/basic-programming/complexity-analysis/time-and-space-complexity/tutorial/
  7. Nour S. Bakr et al.: "DNA Lossless Compression Algorithms: Review", American Journal of Bioinformatics Research, p-ISSN: 2167-6992 e-ISSN: 2167-6976, 2013; 3(3): 72-81, doi:10.5923/j.bioinformatics.20130303.04
  8. Alam Jahaan ,Dr T.N. Ravi, , Dr. S. Panneer Arokiaraj, "Bit DNA Squeezer (BDNAS) : A Unique Technique for Dna Compression", International Journal of Scientific Research in Computer Science, Engineering and Information Technology 2017 IJSRCSEIT | Volume 2 | Issue 4 | ISSN : 2456-3307
  9. Alam Jahaan ,Dr T.N. Ravi, "Single Bit Dna Squeezer (Sbdnas): An Enhancement Of BDNAS Algorithm", International Journal of Scientific Research in Computer Science, Engineering and Information Technology 2017 IJSRCSEIT | Volume 2 | Issue 6 | ISSN : 2456-3307
  10. Rajeswari, P. R., and Apparao, A., 2010," Genbit Compress Tool (GBC): A Java-Based Tool To Compress DNA Sequences and Compute Compression Ratio (BITS/BASE) Of Genomes", International Journal of Computer Science and Information Technology, 2(3)
  11. Rajeswari, P. R., Apparao, A., and Kumar, R. K., 2010, "HUFFBIT COMPRESS Algorithm to compress DNA sequences using extended binary tree", Journal of Theoretical and Applied Information Technology, 13(2), 101-106
  12. Rajeswari, P. R., and Apparao, A., 2011, "DNABIT Compress Genome compression algorithm", Bioinformation, 5(8), 350-360
  13. Satyanvesh, D., Balleda, K., Padyana, A., et al., 2012, "GenCodex - A Novel Algorithm for Compressing DNA sequences on Multi-cores and GPUs", Proc. IEEE, 19th International Conf. on High Performance Computing (HiPC), Pune, India, No 37.
  14. Prasad, V. H., and Kumar, P. V., 2012, "A New Revised DNA Cramp Tool Based Approach of Chopping DNA Repetitive and Non-Repetitive Genome Sequences", International Journal of Computer Science Issues (IJCSI), 9(6), 448-454.
  15. Prasad, V. H., 2013, "A new revisited compression technique through innovation partition group binary compression: a novel approach", International Journal of Computer Engineering & Technology (IJCET), 4(2), 94-101.

IInternational Journal of Scientific Research in Computer Science, Engineering and Information Technology

Downloads

Published

2018-10-30

Issue

Volume 3, Issue 7, September-October-2018

Section

Research Articles

License

Copyright (c) IJSRCSEIT

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

How to Cite

[1]
Dr. S. Panneer Arokiaraj, Alam Jahaan , " Enhanced Single Bit DNA Squeezer (ESBDNAS), IInternational Journal of Scientific Research in Computer Science, Engineering and Information Technology(IJSRCSEIT), ISSN : 2456-3307, Volume 3, Issue 7, pp.345-351, September-October-2018.