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Title

shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction

 

Authors

Nishtha Singh1, Tanmaya Kumar Sahu1, Atmakuri Ramakrishna Rao1* & Trilochan Mohapatra2

 

Affiliation

1Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India, 110 012; 2Central Rice Research Institute, Cuttack, Odisha, India, 753 006.

 

Email

arrao@iasri.res.in; *Corresponding author

 

Article Type

Software

 

Date

Received May 13, 2012; Accepted June 08, 2012; Published July 06, 2012

Abstract

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

http://bioinformatics.iasri.res.in/EDA/downloads/shRNAPred_v1.0.exe

 

Keywords

shRNA, shRNA prediction, RNAi, Gene silencing

 

Citation

Singh et al. Bioinformation 8(13): 629-633 (2012)

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.