A novel representation of protein sequences and its application

Journal of Convergence Information Technology

Volumn 6, Issue 9, 2011, Pages 227-235

  Qian, Panpan ^a   Zhang, Yusen ^a   Jian, Guiqian ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

Phylogenic tree; Relative frequency; Similarity matrix

Indexed keywords

AVIAN INFLUENZA; CORONAVIRUSES; DISTANCE MEASURE; EVOLUTIONARY RELATIONSHIPS; PHYLOGENIC ANALYSIS; PHYLOGENIC TREES; PROTEIN SEQUENCES; RELATIVE FREQUENCIES; SIMILARITY MATRIX; SPIKE PROTEIN;

PLANT EXTRACTS; TWO DIMENSIONAL; VIRUSES;

PROTEINS;

EID: 80053981019     PISSN: 19759320     EISSN: None     Source Type: Journal    
DOI: 10.4156/jcit.vol6.issue9.27     Document Type: Article

References (24)

1. Yusen Zhang, Wei Chen, "Invariants of DNA Sequences Based on 2DD-Curves", Journal of Theoretical Biology, vol. 242, no. 2, pp.382-388, 2006.
2. Yusen Zhang, Bo Liao, Kequan Ding, "On 3DD-Curves of DNA Sequences", Molecular Simulation, vol. 32, no. 1, pp.29-34, 2006.
3. Yusen Zhang, Bo Liao, Kequan Ding, "On 2D Graphical Representation of DNA Sequence of Nondegeneracy", Chemical Physics Letters, vol. 411, no. 1/3, pp.28-32, 2005.
4. Chun Li, Xiaoqing Yu, Nadia Helal, " Similarity analysis of DNA sequences based on codon usage", Chem. Phys. Lett., vol. 459, no. 1/6, pp.172-174, 2008.
5. Yusen Zhang, "A simple method to construct the similarity matrices of DNA sequences", MATCH Commun. Math. Comput. Chem., vol. 60, no. 2, pp.313-324, 2008.
6. Bo Liao, Xuyu Xiang, Wen Zhu, "Coronavirus phylogeny based on 2D graphical representation of DNA sequence", Journal of Computational Chemistry, vol. 27, no. 11, pp.1196-1202, 2006.
7. Bo Liao, Wen Zhu, Yang Liu, "3D graphical representation of DNA sequence without degeneracy and its applications in constructing phylogenic tree", MATCH Communications in Mathematical and in Computer Chemistry, vol. 56, no. 1, pp.209-216, 2006.
8. Huijuan Lu, Wutao Chen, Xiaoping Ma, Mingyi Wang, Jinwei Zhang, Model-free Gene Selection Using Genetic Algorithms, JDCTA, vol. 5, no. 1, pp. 195-203, 2011.
9. Hyoung Do Kim, Ju-Han Kim, DNA Data Compression Based on the Whole Genome Sequence, JCIT: Journal of Convergence Information Technology, vol. 4, no. 3, pp. 82-85, 2009.
10. Bo Liao, BenYou Liao, Xingming Sun, Qingguang Zeng, "A Novel method for similarity analysis and protein subcellular localization prediction", Bioinformatics, vol. 26, no. 21, pp.2678-2683, 2010.
11. Huijuan Lu, Wutao Chen, Xiaoping Ma, Mingyi Wang, Jinwei Zhang, Model-free Gene Selection Using Genetic Algorithms, JDCTA, vol. 5, no. 1, pp. 195-203, 2011.
12. Hyoung Do Kim, Ju-Han Kim, DNA Data Compression Based on the Whole Genome Sequence, JCIT: Journal of Convergence Information Technology, vol. 4, no. 3, pp. 82-85, 2009.
13. Milan Randic, Marjan Vracko, Ashesh Nandy, Subhash C. Basak, "On 3-D graphical representation of DNA primary sequences and their numerical characterization", J. Chem. Inf. Comput. Sci., vol. 40, no. 5, pp.1235-1244, 2000.
14. Milan Randic, Marjan Vracko, Nella Lers, Dejan Plavsi'c, Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation', Chem. Phys. Lett., vol.37, no. 1/2, pp.1202-1207, 2003.
15. Yuhua Yao, Tianming Wang, "A class of new 2-D graphical representation of DNA sequences and their application". Chem. Phys. Lett., vol. 398, no. 4/6, pp.318-323, 2004.
16. Chun Li, Ji Hu, "2-D Graphical representation for characteristic sequences of DNA and its application", J. Biochem. Mol. Biol., vol. 39, no. 3, pp.292-296, 2006.
17. Milan Randic, Xiaofeng Guo, Subhash C. Basak, "On the Characterization of DNA Primary Sequences by Triplet of Nucleic Acid Bases", J. Chem. Inf. Comput. Sci., vol. 41, no. 38, pp.619-626, 2001.
18. Chun Li, Jun Wang, "New Invariant of DNA Sequences", J. Chem. Inf. Model., vol. 45, no. 1, pp.115-120, 2005.
19. Vera Afreixo, Carlos A. C. Bastos, Armando J. Pinho, Sara P. Garcia, Paulo J. S. G. Ferreira, "Genome analysis with inter-nucleotide distances", Bioinformatics, vol. 25, no. 23, pp.3064-3070, 2009.
20. Carolin Rohm, Nannan Zhou, Jochen Suss, John Mackenzie, Robert G. Webster, "Characterization of a novel influenza hemarrlutinin, H15: criteria for determination of influenza A subtypes", Virology, vol. 217, no. 2, pp.508-516, 1996.
21. Yuwei Weng, Yansheng Yan, Yongjun Zhang, Shiqin Yang, Xiaona Shen, "Genome sequencing and analysis of a high pathogenic avian influenza virus strain A/Fujian/1/2007(H5N1) isolated form a patient in Fujian, China", Chin. J. Zoonoses., vol. 7, no. 7, pp.635-638, 2007.
22. The World Health Organization Global Influenza Program Surveillance Network, "Evolution of H5N1 avian influenza viruses in Asia. Emerging infectious diseases", vol. 11, no. 10, pp.1515-5121, 2005.
23. Yanqiu Liu, Yusen Zhang, "A new method for analyzing H5N1 avian influenza virus", J. Math. Chem., vol. 47, no. 3, pp.1129-1141, 2009.
24. Xiufeng Wan, Guorong Chen, Feng Luo, Michael Emch, Ruben Donis, "A quantitative genotype algorithm reflecting H5N1 Avian influenza niche", Bioinformatics, vol. 23, no. 18, pp.2368-2375, 2007.