DV-Curve Representation of Protein Sequences and Its Application
作者： Wei Deng , Yihui Luan
DOI: 10.1155/2014/203871
关键词:
摘要: Based on the detailed hydrophobic-hydrophilic(HP) model of amino acids, we propose dual-vector curve (DV-curve) representation protein sequences, which uses two vectors to represent one alphabet sequences. This graphical not only avoids degeneracy, but also has good visualization no matter how long these sequences are, and can reflect length sequence. Then transform 2D-graphical into a numerical characterization that facilitate quantitative comparison The utility this approach is illustrated by examples: similarity/dissimilarity among different ND6 based their DV-curve figures other phylogenetic analysis coronaviruses spike proteins.
hindawi.com参考文章(44)
M. Randić, M. Vračko, A. Nandy, S. C. Basak, On 3-D graphical representation of DNA primary sequences and their numerical characterization. Journal of Chemical Information and Computer Sciences. ,vol. 40, pp. 1235- 1244 ,(2000) , 10.1021/CI000034Q
Bo Liao, Mingshu Tan, Kequan Ding, Application of 2-D graphical representation of DNA sequence Chemical Physics Letters. ,vol. 414, pp. 296- 300 ,(2005) , 10.1016/J.CPLETT.2005.08.079
Jun Wang, Wei Wang, Modeling study on the validity of a possibly simplified representation of proteins. Physical Review E. ,vol. 61, pp. 6981- 6986 ,(2000) , 10.1103/PHYSREVE.61.6981
Bo Liao, Renfa Li, Wen Zhu, Xuyu Xiang, On the Similarity of DNA Primary Sequences Based on 5-D Representation Journal of Mathematical Chemistry. ,vol. 42, pp. 47- 57 ,(2007) , 10.1007/S10910-006-9091-Z
Moheb I. Abo el Maaty, Mervat M. Abo-Elkhier, Marwa A. Abd Elwahaab, 3D graphical representation of protein sequences and their statistical characterization Physica A-statistical Mechanics and Its Applications. ,vol. 389, pp. 4668- 4676 ,(2010) , 10.1016/J.PHYSA.2010.06.031
T. D. Pham, J. Zuegg, A probabilistic measure for alignment-free sequence comparison Bioinformatics. ,vol. 20, pp. 3455- 3461 ,(2004) , 10.1093/BIOINFORMATICS/BTH426
Rui Chi, Kequan Ding, Novel 4D numerical representation of DNA sequences Chemical Physics Letters. ,vol. 407, pp. 63- 67 ,(2005) , 10.1016/J.CPLETT.2005.03.056
Yu-Hua Yao, Qi Dai, Ling Li, Xu-Ying Nan, Ping-An He, Yao-Zhou Zhang, Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation Journal of Computational Chemistry. ,vol. 31, pp. 1045- 1052 ,(2009) , 10.1002/JCC.21391
LUSHENG WANG, TAO JIANG, On the Complexity of Multiple Sequence Alignment Journal of Computational Biology. ,vol. 1, pp. 337- 348 ,(1994) , 10.1089/CMB.1994.1.337
Bo Liao, Yusen Zhang, Kequan Ding, Tian-ming Wang, Analysis of similarity/dissimilarity of DNA sequences based on a condensed curve representation Journal of Molecular Structure-theochem. ,vol. 717, pp. 199- 203 ,(2005) , 10.1016/J.THEOCHEM.2004.12.015