PREDICTION OF METHANOBACTERIUM USING SUFFIXTREE

Satyasaivani B.¹*, Kaladhar DSVGK², Shashi M.³, Kesavareddy J.^4
1Department of Computer Science, GITAM University, Visakhapatnam, Andhra Pradesh
²Department of Bioinformatics, GITAM University, Visakhapatnam, Andhra Pradesh
³Department Of Computer and Systems Engineering, Andhra University, Visakhapatnam, Andhra Pradesh
⁴Department of Computer science, GITAM University, Visakhapatnam, Andhra Pradesh
* Corresponding Author : vedulvani@yahoo.co.in

Received : -     Accepted : -     Published : 21-12-2009
Volume : 1     Issue : 2       Pages : 1 - 4
Int J Mach Intell 1.2 (2009):1-4
DOI : http://dx.doi.org/10.9735/0975-2927.1.2.1-4

Keywords : Ukkonen’s algorithm, Methanobacterium, MEGA, 16S rRNA
Conflict of Interest : None declared
Acknowledgements/Funding : The author would like to express thanks to Departments of computer science and Bioinformatics, GITAM Institute of science, GITAM University, Visakhapatnam for providing research material and necessary facilities.

Prediction of Methanobacterium using suffix tree is a server designed to know the query sequence related to Methanococus thermophilus and also to execute the maximum length of the string related to Methanococcus. MEGA 4.0 is used to know the conserved sites aligned from 70 sequences related to 16S rRNA nucleotide sequence (Methanococcus thermophilus) from NCBI database. There are 12 strings aligned in all sequences that are highly conserved in the aligned sequences. Ukkonen’s algorithm is used to find the suffix tree for the given patterns (conserved sites). If the query sequence is submitted to the PMST (Prediction of Methanobacterium using Suffix Tree), the results will give the maximum sequence length and the suffix tree based on Ukkonen’s algorithm.

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