دورية أكاديمية
Development of a tool for computational prediction of σ70 promoters in Pseudomonas spp using SVM and HMM approaches
| العنوان: | Development of a tool for computational prediction of σ70 promoters in Pseudomonas spp using SVM and HMM approaches |
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| المؤلفون: | MERIN K ELDO, M K RAJESH, T P JAMSHINATH, N HEMALATHA, MURALI GOPAL, GEORGE V THOMAS |
| المصدر: | The Indian Journal of Agricultural Sciences, Vol 84, Iss 1 (2014) |
| بيانات النشر: | Indian Council of Agricultural Research, 2014. |
| سنة النشر: | 2014 |
| المجموعة: | LCC:Agriculture |
| مصطلحات موضوعية: | HMM, Promoter, Pseudomonas, SVM, σ70, Agriculture |
| الوصف: | 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 s70 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. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 0019-5022 2394-3319 |
| Relation: | https://epubs.icar.org.in/index.php/IJAgS/article/view/37167; https://doaj.org/toc/0019-5022; https://doaj.org/toc/2394-3319 |
| DOI: | 10.56093/ijas.v84i1.37167 |
| URL الوصول: | https://doaj.org/article/8910bdfd8a1a49a0a94d26e252040013 |
| رقم الأكسشن: | edsdoj.8910bdfd8a1a49a0a94d26e252040013 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 00195022 23943319 |
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| DOI: | 10.56093/ijas.v84i1.37167 |