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Understanding Mycobacteriophages through their Unrevealed Proteins
Abstract
The Mycobacteriophages are the bacteriophages infecting different Mycobacterium species in nature. The hypothetical proteins in 17 different Mycobacteriophages were structurally and functionally characterized by using computational tools like CDD-Blast, Interproscan, pfam, COGS and protein structure prediction server (PS2 server). Near about 2188 hypothetical proteins were screened for presence of functional domains and structural classification. The function predictions for 586 hypothetical proteins and structure predictions for 171 hypothetical proteins were possible by using these Bioinformatics web tools. These results can prove helpful for proper understanding of functional, evolutionary and metabolic development of Mycobacterium species.
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References
Alex, B., Lachlan, C., Richard, D., Robert, D. F., Volker, H., Sam, G.J., Ajay, K., Mhairi, M., Simon, M., Erik, L. L. S., David, J. S., Corin Y., Sean, R. E., (2004). The Pfam families’ database. Nucleic Acids Research, Vol. 32, D138-D141.
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J., (1997). Gapped BLAST and PSI-BLAST: ―a new generation of protein database search programs‖. Nucleic Acids Res. 25 (17), 3389-402.
Aron, M. Bauer., John, B. A., Myra, K. D., Carol, D. S., Noreen, R. G., Marc, G., Luning, H., Siqian, H., David, I. H., John, D. J., Zhaoxi, K., Dmitri, K., Christopher, J. L.,Cynthia A. L., Chunlei, L., Fu, L., Shennan, L., Gabriele, H. M., Mikhail, M., James, S. S., Narmada, T., Roxanne, A. Y., Jodie, J. Y., Dachuan, Z., Stephen, H. B., (2006). CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Research, Vol. 35, D237– D240.
Cedric, N., Desmond, G. H., Jaap, H., (2000). T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217.
Chih-Chieh, C., Jenn-Kang, H., Jinn-Moon, Y., (2006). (PS)2: protein structure prediction server Nucl. Acids Res. 34, W152-W157.
Edward, E., Gary, L. G., Osnat, H., John, M., John, O., Roberto, J. P., Linda, B., Delwood, R., Andrew, J. H., (2000). Biological function made crystal clear- annotation of hypothetical proteins via structural genomics. Current Opinion in Biotechnology 11, 25-30.
Gough J, Karplus K, Hughey R, Chothia C (2001). Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 2001 Nov 2;313(4):903-19
Roman, L. T., Michael, Y., Galperin, Darren A. Natale, Eugene V. Koonin (2000). The COG database: a tool for genome –scale analysis of protein functions and evolution. Nucleic Acid Research. 28, 33-36.
Sanmukh S. G., Paunikar W. N. and Ghosh T. K. (2011). Computational approach for structure and functionality search for hypothetical proteins in Mycobacterium leprae. CiiT International Journal of Data Mining Knowledge Engineering
Sanmukh S. G., Paunikar W. N. and Ghosh T. K. (2011). Study of Hypothetical Proteins in Salmonella Phages and Predicting their Structural and Functional Relationship. CiiT International Journal of Biometrics and Bioinformatics.
Sanmukh S. G., Paunikar W. N., Ghosh T. K., Chakrabarti T. Structure and function prediction of hypothetical proteins in Vibriophages. Inter. J. of Biometric and Bioinformatics vol.4 (5). (Published Online) 2010.
Schaffer, A. A., Aravind, L., Madden, T. L., Shavirin, S. Spouge, J. L., Wolf, Y. I., Koonin, E. V., Altschul, S. F., (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29(14), 2994- 3005.
Wendy, B. et al., (2000). The EMBL Nucleotide Sequence Database. Nucleic Acid Research. 28, 19-23
Zafer, A., Yucel, A., Mark, B., (2006). ―Protein secondary structure prediction for a single sequence using hidden semi-Markov models, BMC Bioinformatics, ―7, 178.
Zdobnov, E. M., Rolf, A., (2001). Interproscan- an integration platform for the signatures recognition methods in InterPro. Bioinformatics 17, 847-848
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