Genomic and proteomic repository of chitin degrading bacterium Serratia proteamaculans 568
DOI:
https://doi.org/10.26438/ijcse/v5i9.5254Keywords:
Serratia proteomaculans 568, gene sequences, protein sequences, physico-chemical properties, Secondary structuresAbstract
In this paper, we describe about a repository which is composed of the information related to genes sequences, proteins sequences, upstream sequences, codon usage in proteins, physico-chemical properties, secondary structures and biochemical pathway information of proteins of chitin degrading bacterium Serratia proteomaculans 568. The advantage of this repository is that it can be hosted in the user’s computer and work without internet connection. The backend data for developing this repository was generated using different computational tools which were published earlier. The .faa, .fna, .ptt files of S.proteomaculans 568 were downloaded from NCBI was used as primary seed data for the generation backend data. Web technologies were used to retrieve and display the compiled data in the browser. The data retrieved out of this repository can be used as preliminary source for understanding various concepts related to genes and proteins of Serratia proteomaculans 568. This repository can be obtained from http://crraoaimscs.res.in/serratia_568/serratia_568.rar
References
. S. Taghavi, C. Garafola, S. Monchy, L. Newman, A. Hoffman, N. Weyens, T. Barac, J. Vangronsveld, D. van der Lelie, "Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees", Applied and environmental microbiology, Vol.75, Issue.3, pp.748-757,2009.
. P. Purushotham, P.V. Arun, J.S. Prakash, A.R. Podile, "Chitin binding proteins act synergistically with chitinases in Serratia proteamaculans 568", PloS one, Vol.7, Issue.5, pp.e36714, 2012.
. M. Nakao, S. Okamoto, M. Kohara, T. Fujishiro, T. Fujisawa, S. Sato, S. Tabata, T. Kaneko, Y. Nakamura, “CyanoBase: the cyanobacteria genome database update 2010”, Nucleic acids research, Vol.38, Issue.-, pp.D379-381, 2010.
. P.V. Arun, R.K. Bakku, M. Subhashini, P. Singh, N.P. Prabhu, I. Suzuki, J.S. Prakash, “CyanoPhyChe: a database for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins”, PloS one, Vol.7, Issue.11, pp.e49425, 2012.
. P. Rice, I. Longden, A. Bleasby, “EMBOSS: the European Molecular Biology Open Software Suite, Trends in genetics : TIG”, Vol.16, Issue.6, pp.276-277, 2000.
. D. Frishman, P. Argos, “Seventy-five percent accuracy in protein secondary structure prediction”, Proteins, Vol.27, Issue.3, pp.329-335, 1997.
. A.R. Wattam, D. Abraham, O. Dalay, T.L. Disz, T. Driscoll, J.L. Gabbard, J.J. Gillespie, R. Gough, D. Hix, R. Kenyon, D. Machi, C. Mao, E.K. Nordberg, R. Olson, R. Overbeek, G.D. Pusch, M. Shukla, J. Schulman, R.L. Stevens, D.E. Sullivan, V. Vonstein, A. Warren, R. Will, M.J. Wilson, H.S. Yoo, C. Zhang, Y. Zhang, B.W. Sobral, “PATRIC, the bacterial bioinformatics database and analysis resource”, Nucleic acids research, Vol.42, Issue.- pp.D581-591, 2014.
. I. Ahn, B.J. Jeong, S.E. Bae, J. Jung, H.S. Son, “Genomic analysis of influenza A viruses, including avian flu (H5N1) strains”, Eur J Epidemiol, Vol.21, Issue.7, pp.511-519, 2006.
. J.F. Kane, “Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli”, Curr Opin Biotechnol, Vol.6, Issue.5, pp.494-500, 1995.
. X. Yang, X. Luo, X. Cai, “Analysis of codon usage pattern in Taenia saginata based on a transcriptome dataset”, Parasit Vectors, Vol.7, Issue.1, pp.527, 2014.
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors contributing to this journal agree to publish their articles under the Creative Commons Attribution 4.0 International License, allowing third parties to share their work (copy, distribute, transmit) and to adapt it, under the condition that the authors are given credit and that in the event of reuse or distribution, the terms of this license are made clear.
