An alignment-free method to find similarity among protein sequences via the general form of Chou's pseudo amino acid composition

SAR and QSAR in Environmental Research

Volumn 24, Issue 7, 2013, Pages 597-609

  Gupta, M K ^a   Niyogi, R ^a   Misra, M ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY ROORKEE   (India)

Author keywords

alignment free method; cosine distance metric; phylogenetic tree; sequence similarity analysis

Indexed keywords

INDIUM COMPOUNDS; PHYLOGENETIC; PROTEINS; TREES (MATHEMATICS);

ALIGNMENT-FREE; ALIGNMENT-FREE METHOD; AMINO-ACIDS; COSINE DISTANCE METRIC; DISTANCE METRICS; PHYLOGENETIC TREES; PROTEIN SEQUENCES; SEQUENCE SIMILARITY; SEQUENCE SIMILARITY ANALYSE; SIMILARITY ANALYSIS;

AMINO ACIDS;

CORONAVIRUS;

EID: 84888000439     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/1062936X.2013.773378     Document Type: Article

References (37)

1. Chou, K.-C. and Shen, H.-B. 2007. Recent progress in protein subcellular location prediction. Anal. Biochem., 370: 1 - 16.
2. Z. He, J. Zhang, X.-H. Shi, L.-L. Hu, X. Kong, Y.-D. Cai, and K.-C. Chou, Predicting drug-target interaction networks based on functional groups and biological features, PLoS ONE 5 (2010), pp. 1-8.
3. Huang, T., Niu, S., Xu, Z., Huan, Y., Kong, X., Cai, Y.-D. and Chou, K.-C. 2011. Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties. PLoS ONE, 6: 1 - 8.
4. Chen, W., Lin, H., Feng, P.-M., Ding, C., Zuo, Y.-C. and Chou, K.-C. 2012. INuc-PhysChem: A sequence-based predictor for identifying nucleosomes via physicochemical properties. PLoS ONE, 7: 1 - 9.
5. Chou, K.-C. 1996. Prediction of human immunodeficiency virus protease cleavage sites in proteins. Anal. Biochem., 233: 1 - 14.
6. Hu, L.-L., Huang, T., Cai, Y.-D. and Chou, K.-C. 2011. Prediction of body fluids where proteins are secreted into based on protein interaction network. PLoS ONE, 6: 1 - 8.
7. Huang, T., Shi, X.-H., Wang, P., He, Z., Feng, K.-Y., Hu, L.L., Kong, X., Li, Y.-X., Cai, Y.-D. and Chou, K.-C. 2010. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE, 5: 1 - 9.
8. Chou, K.-C., Wu, Z.-C. and Xiao, X. 2011. iLoc-Euk: A multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS ONE, 6: 1 - 10.
9. Chou, K.-C., Wu, Z.-C. and Xiao, X. 2012. iLoc-Hum: Using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites. Mol. BioSyst., 8: 629 - 641.
10. Wang, P., Hu, L., Liu, G., Jiang, N., Chen, X., Xu, J., Zheng, W., Li, L., Tan, M., Chen, Z., Song, H., Cai, Y.-D. and Chou, K.-C. 2011. Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS ONE, 6: 1 - 9.
11. Wang, P., Xiao, X. and Chou, K.-C. 2011. NR-2L: A two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features. PLoS ONE, 6: 1 - 9.
12. Li, B.-Q., Huang, T., Liu, L., Cai, Y.-D. and Chou, K.-C. 2012. Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network. PLoS ONE, 7: 1 - 12.
13. Huang, T., Wang, J., Cai, Y.-D., Yu, H. and Chou, K.-C. 2012. Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma. PLoS ONE, 7: 1 - 9.
14. Li, B.-Q., Hu, L.-L., Niu, S., Cai, Y.-D. and Chou, K.-C. 2012. Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches. J. Proteomics, 75: 1654 - 1665.
15. Chou, K.-C. 2004. Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 11: 2105 - 2134.
16. Hamori, E. and Ruskin, J. 1983. H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem., 258: 1318 - 1327.
17. Gates, M.A. 1986. A simple way to look at DNA. J. Theor. Biol., 119: 319 - 328.
18. Nandy, A. 1994. A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to globin genes. Curr. Sci., 66: 309 - 314.
19. Leong, P.M. and Morgenthaler, S. 1995. Random walk and gap plots of DNA sequences. Comput. Appl. Biosci., 11: 503 - 507.
20. Randić, M. 2004. 2-D Graphical representation of proteins based on virtual genetic code. SAR QSAR Environ. Res., 15: 147 - 157.
21. Randić, M., Vračko, M., Novič, M. and Plavšić, D. 2009. Spectral representation of reduced protein models. SAR QSAR Environ. Res., 20: 415 - 427.
22. Randić, M., Mehulić, K., Vukičević, D., Pisanski, T., Vikić-Topić, D. and Plavšić, D. 2009. Graphical representation of proteins as four-color maps and their numerical characterization. J. Mol. Graph. Model., 27: 637 - 641.
23. Feng, J. and Wang, T.M. 2008. Characterization of protein primary sequences based on partial ordering. J. Theor. Biol., 254: 752 - 755.
24. Randić, M., Novič, M. and Vračko, M. 2008. On novel representation of proteins based on amino acid adjacency matrix. SAR QSAR Environ. Res., 19: 339 - 349.
25. Chou, K.-C. 2011. Some remarks on protein attribute prediction and pseudo amino acid composition. J. Theor. Biol., 273: 236 - 247.
26. Chou, K.-C. 2001. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins: Struct Funct. Bioinf., 43: 246 - 255.
27. Chou, K.-C. 2005. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics, 21: 10 - 19.
28. Liu, L., Ho, Y.-K. and Yau, S. 2006. Clustering DNA sequences by feature vectors. Mol. Phylogenet. Evol., 41: 64 - 69.
29. Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4: 406 - 425.
30. Xing, L., Li, C. and Wang, X. 2008. 2-D graphical representation of protein sequences and its application to coronavirus phylogeny. BMB Rep., 41: 217 - 222.
31. Kumar, S., Nei, M., Dudley, J. and Tamura, K. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinf., 9: 299 - 306.
32. Li, M., Badger, J.H., Chen, X., Kwong, S., Kearney, P. and Zhang, H. 2001. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics, 17: 149 - 154.
33. Wen, J. and Zhang, Y. 2009. A 2D graphical representation of protein sequence and its numerical characterization. Chem. Phys. Lett., 476: 281 - 286.
34. Abo el Maaty, M.I., Abo-Elkhier, M.M. and Abd Elwahaab, M.A. 2010. 3D graphical representation of protein sequences and their statistical characterization. Physica A, 389: 4668 - 4676.
35. Abo-Elkhier, M.M. 2012. Similarity/dissimilarity analysis of protein sequences using the spatial median as a descriptor. J. Biophys. Chem., 3: 142 - 148.
36. Wu, Z.-C., Xiao, X. and Chou, K.-C. 2010. 2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. J. Theor. Biol., 267: 29 - 34.
37. Chou, K.-C. and Shen, H.-B. 2009. Recent advances in developing web-servers for predicting protein attributes. Nat. Sci., 1: 63 - 92.