Introduction

UNLABELLED: The small hairpin RNAs (shRNA) are useful in many ways like identification of trait specific molecular markers, gene silencing and characterization of a species. In public domain, hardly there exists any standalone software for shRNA prediction. Hence, a software shRNAPred (1.0) is proposed here to offer a user-friendly Command-line User Interface (CUI) to predict 'shRNA-like' regions from a large set of nucleotide sequences. The software is developed using PERL Version 5.12.5 taking into account the parameters such as stem and loop length combinations, specific loop sequence, GC content, melting temperature, position specific nucleotides, low complexity filter, etc. Each of the parameters is assigned with a specific score and based on which the software ranks the predicted shRNAs. The high scored shRNAs obtained from the software are depicted as potential shRNAs and provided to the user in the form of a text file. The proposed software also allows the user to customize certain parameters while predicting specific shRNAs of his interest. The shRNAPred (1.0) is open access software available for academic users. It can be downloaded freely along with user manual, example dataset and output for easy understanding and implementation. AVAILABILITY: The database is available for free at http://bioinformatics.iasri.res.in/EDA/downloads/shRNAPred_v1.0.exe.

Publications

  1. shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction.
    Cite this
    Singh N, Sahu TK, Rao AR, Mohapatra T, 2012-01-01 - Bioinformation

Credits

  1. Nishtha Singh
    Developer

  2. Tanmaya Kumar Sahu
    Developer

  3. Atmakuri Ramakrishna Rao
    Developer

  4. Trilochan Mohapatra
    Investigator

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Summary
AccessionBT003307
Tool TypeApplication
Category
PlatformsWindows
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByTrilochan Mohapatra