64
Views
3
CrossRef citations to date
0
Altmetric
Articles

Efficient implementation of parametric spectral estimation techniques for DNA exon prediction

, , &
Pages 1200-1221 | Received 05 Nov 2019, Accepted 06 Jun 2020, Published online: 01 Jul 2020

References

  • Attwood, T.; Miller, C. Progress in Bioinformatics and the Importance of Being Earnest. Biotechnol. Annu. Rev. 2002, 8, 1–54. DOI: 10.1016/s1387-2656(02)08003-1.
  • Luscombe, N. M.; Greenbaum, D.; Gerstein, M. What is Bioinformatics? A Proposed Definition and Overview of the Field. Methods Inf. Med. 2001, 40, 346–358. DOI: 10.1055/s-0038-1634431.
  • Anastassiou, D. Genomic Signal Processing. IEEE Signal Process. Mag. 2001, 18, 8–20. DOI: 10.1109/79.939833.
  • El-Badawy, I. M.; Gasser, S.; Aziz, A. M. 2015 On the Use of pseudo-EIIP Mapping Scheme for Identifying Exons Locations in DNA Sequnces. IEEE International Conference on Signal and Image Processing Applications (ICSIPA).
  • Inbamalar, T.; Sivakumar, R. Study of DNA Sequence Analysis Using DSP Techniques. JOACE. 2013, 1, 336–342. Vol, P. DOI: 10.12720/joace.1.4.336-342.
  • Saberkari, H.; Shamsi, M.; Heravi, H.; Sedaaghi, M. H. A Fast Algorithm for Exonic Regions Prediction in DNA Sequences. J. Med. Signals Sens. 2013, 3, 139–147. DOI: 10.4103/2228-7477.120977.
  • Saberkari, H.; et al. Prediction of Protein Coding Regions in DNA Sequences Using Signal Processing Techniques. In Industrial Electronics and Applications (ISIEA), IEEE Symposium on; 2012; p. 355–360.
  • Dessouky, A. M.; Taha, T. E.; Dessouky, M. M.; Eltholth, A. A.; Hassan, E.; Abd El-Samie, F. E. Non-Parametric Spectral Estimation Techniques for DNA Sequence Analysis and Exon Region Prediction. Computers Electr Eng. J. 2019, 73, 334–348. DOI: 10.1016/j.compeleceng.2018.12.001.
  • Dessouky, A. M.; Taha, T. E.; Dessouky, M. M.; Eltholth, A. A.; Hassan, E.; Samie, F. E. A. E. Visual Representation of DNA Sequences for Exon Detection Using Non-Parametric Spectral Estimation Techniques. Nucleosides, Nucleotides Nucleic Acid J., 2019, 38, 321–337. (Taylor and Francis).
  • Proakis, J. G.; Rader, C. M.; Ling, F.; Nikias, C. L. Advanced Digital Signal Processing; Maxwell Macmillan International: New York, 1992.
  • Orfanidis, S. J. Optimum Signal Processing: An Introduction; New York, USA: Mcgraw-Hill Book Company, 1990.
  • Kalouptsidis, N. Signal Processing Systems, Theory and Design; New York, USA: John Wiely And Sons, Inc, 1997.
  • Zelniker, G.; Taylor, F. J. Advanced Digital Signal Processing: Theory and Applications; Marcel Dekker, Inc.: New York, 1994.
  • Robinson, E. A. A Historical Perspective of Spectrum Estimation. Proc. IEEE 1982, 70, 885–907. DOI: 10.1109/PROC.1982.12423.
  • Wassfy, H. M.; Salem, M. L.; Abdelnaby, M. M.; Mabrouk, M. S.; Zidan, A. Advanced DNA Mapping Schemes for Exon Prediction Using Digital Filters. Am. J. Biomed. Eng. 2016, 6, 25–31.
  • Berger, J.; Mitra, S.; J. Astola. Power Spectrum Analysis for DNA Sequences. In Signal Processing and Its Applications, Proceedings. Seventh International Symposium, IEEE, 2003; p. 29–32.
  • Wąż, P.; Bielińska-Wąż, D. Non-Standard Similarity/Dissimilarity Analysis of DNA Sequences. Genomics 2014, 104, 464–471. DOI: 10.1016/j.ygeno.2014.08.010.
  • Bielińska-Wąż, D. Graphical and Numerical Representations of DNA Sequences: Statistical Aspects of Similarity. J. Math. Chem. 2011, 49, 2345–2407. DOI: 10.1007/s10910-011-9890-8.
  • Hassan, M. S.; Shaalan, A. A.; Dessouky, M. I.; Abdelnaiem, A. E.; ElHefnawi, M. Evaluation of Computational Techniques for Predicting Non-Synonymous Single Nucleotide Variants Pathogenicity. Genomics, Elsevier 2019, 111, 869–882. DOI: 10.1016/j.ygeno.2018.05.013.
  • Hassan, M. S.; Shaalan, A. A.; Dessouky, M. I.; Abdelnaiem, A. E.; Abdel-Haleem, D. A.; ElHefnawi, M. Predicting Non-Synonymous Single Nucleotide Variants Pathogenic Effects in Human Diseases. Encyclopedia Bioinform. Comput. Biol. 2016, 3, 400–409. doi: 10.1016/b978-0-12-809633-8.90692-7.
  • Hassan, M. S.; Shaalan, A. A.; Dessouky, M. I.; Abdelnaiem, A. E.; ElHefnawi, M. A Review Study: Computational Techniques for Expecting the Impact of Non-Synonymous Single Nucleotide Variants in Human Diseases. Gene 2019, 680, 20–33. DOI: 10.1016/j.gene.2018.09.028.
  • Abo-Zahhad, M.; Ahmed, S. M.; Abd-Elrahman, S. A. Genomic Analysis and Classification of Exon and Intron Sequences Using DNA Numerical Mapping Techniques. IJITCS. 2012, 4, 22–36. DOI: 10.5815/ijitcs.2012.08.03.
  • Mabrouk, M. S. A Study of the Potential of EIIP Mapping Technique in Exon Prediction Using the Frequency Domain Techniques. Am. J. Biomed. Eng. 2012, 2, 17–22.
  • Nair, A. S.; Sreenadhan, S. P. A Coding Measure Scheme Employing Electron-Ion Interaction Pseudopotential (EIIP). Bioinformation 2006, 1, 197–202.
  • Yin, C.; Yau, S. S.-T. Numerical Representation of DNA Sequences Based on Genetic Code Context and Its Applications in Periodicity Analysis of Genomes. In Computational Intelligence in Bioinformatics and Computational Biology, IEEE Symposium on 2008, 223–227.
  • Bai Arniker, S.; Kwan, H. K. Advanced Numerical Representation of DNA Sequences. In International Conference on Bioscience, Biochemistry and Bioinformatics IPCBEE 2012, 31, 2–5.
  • https://srogic.wordpress.com/datasets/hmr195-dataset/. (accessed May 18, 2020).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.