Browsing by Author "Jamshinath, T.P."
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Item Development of a tool for computational prediction of σ70 promoters in Pseudomonas spp using SVM and HMM approaches(2014) Merin K. Eldo; Rajesh, M.K.; Jamshinath, T.P.; Hemalatha, N.; Murali Gopal; George V. ThomasPromoters 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.Item Homology modeling deduced 3-D structure of adenylation domain of Pseudomonas fluorescens Pf-5 non-ribosomal peptide synthesis (NRPS)(2012-11) Jamshinath, T.P.; Philip Job, N.; Rajesh, M.K.; Murali Gopal; George V. ThomasItem LTTRPred: A tool for prediction of transcriptional regulator of pyoluteorin pathway in Pseudomonas species using SVM-based approach(2012-11) Anil Paul; Rajesh, M.K.; Hemalatha, N.; Jamshinath, T.P.; Murali Gopal; George V. ThomasItem A Machine Learning Approach for Discovery of Novel Non- Ribosomal Peptide Synthetases (NRPS) in genomes of Plant Growth Promoting Pseudomonas Spp(2014-10) Philip Job, N.; Jamshinath, T.P.; Hemalatha, N.; Rajesh, M.K.Non-ribosomal peptide synthetases (NRPSs) are multi-modular megasynthasespossessing the ability to catalyze biosynthesis of small bioactive peptides through a thiotemplate mechanismwhich is independent of ribosomes. These enzymes are invovled in production of a wide range of chemical products of broad structural and biological activity. The present study was performed with an aim to develop a gene prediction tool using a machine learning work bench called WEKA (Waikato Environment for Knowledge Analysis) for NRPS in plant growth promoting Pseudomonas spp.First, a model was developed using the training data which was generated using many classifiers. The trained model was then used for the prediction of NRPS in a given set of unknown sequences. Cross-validation results showed that the ‘Logistic of Functions’ was the best classifier when compared to others, showing high accuracy and performance in classifying the instances. We hope that the tool will aid in discovering of novel NRPS by predicting them from sequence data obtained by whole genome sequencing of bacteria or metagenomics.Item MAPS: A web-based tool for detection of microsatellites in whole genome sequences(2015) Jamshinath, T.P.; Naganeeswaran, S.; Jomon K. Jose; Rajesh, M.KItem Virtual screening and in vitro evaluation of potential growth regulators against somatic embryogenesis receptor- like kinase(SERK) in Cocos nucifera L.(2015) Rajesh, M.K.; Gangaraj, K.P.; Jamshinath, T.P.; Fayas, T.P.; Naganeeswaran, S.; Sajini, K.K.; Anitha Karun