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International Journal of Computational Bioinformatics and In Silico Modeling
2013: Volume-2 Issue-2
ISSN: 2320-0634

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ABSTRACT   REFERENCES  
International Journal of Computational Bioinformatics and In Silico Modeling 2(2) 2013: 89-93

Modified Pattern Matching (MPM) Algorithm for Detecting the Ribosome Binding Sites: Trends for Bioinformatics Analysis of Escherichia coli K-12 (MG 1655) Genome


Junaid Bin Ahsan1, Adnan Mannan2 , Rasel Das3, Muhammad Ibrahim Khan1 and Md. Arifuzzaman*4

1Department of Computer Science & Engineering, Chittagong University of Engineering & Technology, Chittagong, Bangladesh.
2Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong-4331, Bangladesh.
3Nanotechnology and Catalysis Research Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia.
4Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Chittagong, Bangladesh.

* Corresponding Author

ABSTRACT

Shine-Dalgarno (SD) sequence is found just 5' to the translation initiation codon, part or all of a polypurine domain UAAGGAGGU is found in the prokaryotic mRNA ribosome binding site (RBS). The importance of the SD sequence for identification of the translation initiation site on the mRNA by the ribosome is very much clear, and thereby, translational efficiency is strongly affected by the spacing between the SD and the initiation codon. Although, whether there is a unique optimal spacing is not as clear. The definitions of the spacing as well as secondary structures have been complicated and obscured matters. A systematic study installed by the development of a novel modified algorithmic approach to detect the most probable RBS which is located at upstream of any gene of E. coli genome were undertaken by us, and in addition we have also developed an algorithm which picks up the absolute spacers between each RBS and AUG start codon. Moreover, in order to determine their expression rate in E. coli K-12 (MG1655) genomes all genes on the basis of their spacer lengths between RBS and AUG start codons of that gene were classified. A new insight to disclose the actual happening and ambiguity of E. coli K-12 (Mg1655) genome in a more efficient manner might be provided by this global gene analysis.

Copyright © 2013 | AIZEON publishers | All rights reserved

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Citation: Ahsan JB et al. (2013). Modified Pattern Matching (MPM) Algorithm for Detecting the Ribosome Binding Sites: Trends for Bioinformatics Analysis of Escherichia coli K-12 (MG 1655) Genome. Int J Comput Bioinfo In Silico Model 2(2): 89-93

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