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

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...

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Main Authors:	Singh, Nishtha, Sahu, Tanmaya Kumar, Rao, Atmakuri Ramakrishna, Mohapatra, Trilochan
Format:	Online
Language:	English
Published:	Biomedical Informatics 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400981/

id	pubmed-3400981
recordtype	oai_dc
spelling	pubmed-34009812012-07-24 shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction Singh, Nishtha Sahu, Tanmaya Kumar Rao, Atmakuri Ramakrishna Mohapatra, Trilochan Software 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. Biomedical Informatics 2012-07-06 /pmc/articles/PMC3400981/ /pubmed/22829744 http://dx.doi.org/10.6026/97320630008629 Text en © 2012 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Singh, Nishtha Sahu, Tanmaya Kumar Rao, Atmakuri Ramakrishna Mohapatra, Trilochan
spellingShingle	Singh, Nishtha Sahu, Tanmaya Kumar Rao, Atmakuri Ramakrishna Mohapatra, Trilochan shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction
author_facet	Singh, Nishtha Sahu, Tanmaya Kumar Rao, Atmakuri Ramakrishna Mohapatra, Trilochan
author_sort	Singh, Nishtha
title	shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction
title_short	shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction
title_full	shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction
title_fullStr	shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction
title_full_unstemmed	shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction
title_sort	shrnapred (version 1.0): an open source and standalone software for short hairpin rna (shrna) prediction
description	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.
publisher	Biomedical Informatics
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400981/
_version_	1611544191400148992

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

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