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

Nishtha Singh,Tanmaya Kumar Sahu,Trilochan Mohapatra,Atmakuri Ramakrishna Rao

doi:10.6026/97320630008629

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.AvailabilityThe database is available for free at http://bioinformatics.iasri.res.in/EDA/downloads/shRNAPred_v1.0.exe

Highlights

A small hairpin RNAs (shRNA) is a tight hairpin turn, with a loop of 4–23 nucleotides and a stem of 19–29 nucleotide base pairs [1]. shRNAs are pivotal in the field of gene silencing as these are cheaper than siRNAs for large-scale studies [2]
Initially, different properties of shRNA, like, stem and loop lengths, perfect stem complementarity, GC content, melting temperature (Tm), position specific nucleotides and low complexity regions are taken into consideration while developing the script for shRNAPred
The executable file was generated by using Perl Packager module, provided by Perl Archive Toolkit (PAR) version 0.85_01 of ISSN 0973-2063 0973-8894

Summary

Background

A shRNA is a tight hairpin turn, with a loop of 4–23 nucleotides and a stem (two anti parallel strands) of 19–29 nucleotide base pairs [1]. shRNAs are pivotal in the field of gene silencing as these are cheaper than siRNAs for large-scale studies [2]. Currently available web-based tools fail to predict shRNAs from a large set of nucleotide sequences. The aim of this paper is to develop standalone software, to facilitate prediction of ‘shRNA-like’ regions, by considering an exhaustive list of hairpin parameters, from voluminous genomic sequence data. This software will cater the needs of the researchers and scientists working in the field of RNA interference in designing shRNA. Methodology: Initially, different properties of shRNA, like, stem and loop lengths, perfect stem complementarity, GC content, melting temperature (Tm), position specific nucleotides and low complexity regions are taken into consideration while developing the script for shRNAPred (version 1.0). The executable file was generated by using Perl Packager (pp) module, provided by Perl Archive Toolkit (PAR) version 0.85_01 of ISSN 0973-2063 (online) 0973-8894 (print)

BIOINFORMATION open access

Specific Loop Sequence Reference