CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers

BACKGROUND: Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRNAs and no tool to determine the specificity of circRNA primers. RESULTS: In thi...

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Detalles Bibliográficos
Autores principales: Zhong, Shanliang, Wang, Jinyan, Zhang, Qian, Xu, Hanzi, Feng, Jifeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090782/
https://www.ncbi.nlm.nih.gov/pubmed/30075703
http://dx.doi.org/10.1186/s12859-018-2304-1
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author Zhong, Shanliang
Wang, Jinyan
Zhang, Qian
Xu, Hanzi
Feng, Jifeng
author_facet Zhong, Shanliang
Wang, Jinyan
Zhang, Qian
Xu, Hanzi
Feng, Jifeng
author_sort Zhong, Shanliang
collection PubMed
description BACKGROUND: Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRNAs and no tool to determine the specificity of circRNA primers. RESULTS: In this study, we present circPrimer, which allows users to search, annotate, and visualize circRNAs. Additionally, circPrimer enables users to extract the spliced sequences and genomic sequences of any circRNA, including novel circRNAs. Furthermore, circPrimer help users to design primers for circRNAs and to determine the specificity of the circRNA primers. CONCLUSIONS: CircPrimer is a user-friendly tool for exploring circRNAs that does not require special user skills.
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spelling pubmed-60907822018-08-17 CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers Zhong, Shanliang Wang, Jinyan Zhang, Qian Xu, Hanzi Feng, Jifeng BMC Bioinformatics Software BACKGROUND: Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRNAs and no tool to determine the specificity of circRNA primers. RESULTS: In this study, we present circPrimer, which allows users to search, annotate, and visualize circRNAs. Additionally, circPrimer enables users to extract the spliced sequences and genomic sequences of any circRNA, including novel circRNAs. Furthermore, circPrimer help users to design primers for circRNAs and to determine the specificity of the circRNA primers. CONCLUSIONS: CircPrimer is a user-friendly tool for exploring circRNAs that does not require special user skills. BioMed Central 2018-08-03 /pmc/articles/PMC6090782/ /pubmed/30075703 http://dx.doi.org/10.1186/s12859-018-2304-1 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Zhong, Shanliang
Wang, Jinyan
Zhang, Qian
Xu, Hanzi
Feng, Jifeng
CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers
title CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers
title_full CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers
title_fullStr CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers
title_full_unstemmed CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers
title_short CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers
title_sort circprimer: a software for annotating circrnas and determining the specificity of circrna primers
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090782/
https://www.ncbi.nlm.nih.gov/pubmed/30075703
http://dx.doi.org/10.1186/s12859-018-2304-1
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