Evaluation of Plant Small-RNA Target Prediction Tools for Developing a Pipeline for Genome Wide Identification of Targets

Taraka Ramji, Moturu (2013) Evaluation of Plant Small-RNA Target Prediction Tools for Developing a Pipeline for Genome Wide Identification of Targets. Masters thesis, Indian Institute of Science Education and Research Kolkata.

PDF (MS Dissertation of Moturu Taraka Ramji (11IP03)) MoturuTarakaRamji-11IP03-MSThesis.pdf - Submitted Version Restricted to Repository staff only Download (1MB)

Abstract

Emerging next generation sequencing demands software tools optimum for the prediction of small RNA (smRNA) targets. With increasing number of experimentally validated smRNA targets, plant specific tools have started emerging and critical evaluation of these tools has become the need of the hour. In the present study, we have evaluated the plant specific tools and other popular tools on the experimentally validated smRNA-target interactions based on the parameters and algorithms used in the prediction. Further to improve the performance of the tools, combinations of tools was done. The results would aid researchers in efficient use of different tools individually and in combinations for both Arabidopsis and non-Arabidopsis species. The study points the species bias in the predictions of the tools and the transcript length bias by the usage of free energy parameter. The study also analysed the interactions which were not predicted by the tools to improve the prediction.

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