IISER Kolkata ePrints Repository

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.

[img] PDF (MS Dissertation of Moturu Taraka Ramji (11IP03)) - Submitted Version
Restricted to Repository staff only

Download (1944Kb)

    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.

    Item Type: Thesis (Masters)
    Additional Information: Supervisor: Dr. Shree Prakash Pandey
    Uncontrolled Keywords: Plant; Small RNA; Target Prediction Tools;Genome Wide Identification of Targets; smRNA; smRNA Targets
    Subjects: Q Science > QH Natural history > QH301 Biology
    Divisions: Faculty of Medicine, Health and Life Sciences > School of Biological Sciences
    Depositing User: IISER Kolkata Librarian
    Date Deposited: 14 May 2013 15:49
    Last Modified: 12 Nov 2014 10:31
    URI: http://eprints.iiserkol.ac.in/id/eprint/80

    Actions (login required)

    View Item