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Development of a tool for computational prediction of σ70 promoters in Pseudomonas spp using SVM and HMM approaches

Indian Agricultural Research Journals

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Title Development of a tool for computational prediction of σ70 promoters in Pseudomonas spp using SVM and HMM approaches
 
Creator ELDO, MERIN K
RAJESH, M K
JAMSHINATH, T P
HEMALATHA, N
GOPAL, MURALI
THOMAS, GEORGE V
 
Subject HMM, Promoter, Pseudomonas, SVM, σ70
 
Description Promoters are regions in DNA that play important role in the regulation of gene expression. The ability to locate promoters within a section of DNA is known to be a very difficult and important task in DNA analysis. Since experimental techniques to identify promoters are costly and time consuming, in silico methods offer an alternative. In this study, we have developed a tool for identification of σ70 promoters in the –10 and –35 regions of sequences from Pseudomonas spp. Promoters were predicted using both Support Vector Machine (SVM) and Hidden Markov Model (HMM) based approaches. SVM performed better when trained using RBF kernel with a cross-validation of 5 and a value of 0.03 for the gamma parameter. The module developed using SVM showed a sensitivity of 78% and a specificity of 80%. The programmes required to process the user input were written using Perl and HTML codes were used to create a user interface. The user interface accepts a query sequence and the processed result will be displayed in a new window. The tool named ‘PROMIT’ (PROMoter Identification Tool), was developed in the Windows platform, has a user friendly interface and works well for sequences from Pseudomonas spp.
 
Publisher The Indian Journal of Agricultural Sciences
 
Contributor —
 
Date 2014-01-28
 
Type info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Peer-reviewed Article
 
Format application/pdf
 
Identifier http://epubs.icar.org.in/ejournal/index.php/IJAgS/article/view/37167
 
Source The Indian Journal of Agricultural Sciences; Vol 84, No 1 (2014)
0019-5022
 
Language eng
 
Relation http://epubs.icar.org.in/ejournal/index.php/IJAgS/article/view/37167/16605
 
Rights Copyright (c) 2014 The Indian Journal of Agricultural Sciences