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

descriptionPublicationkeyboard_double_arrow_right Article , Other literature type 03 Aug 2018 English Publisher:Springer Science and Business Media LLCJournal:BMC Bioinformatics, volume 19 (eissn: 1471-2105, Copyright policy )
Authors: Shanliang Zhong; Jinyan Wang; Qian Zhang; Hanzi Xu; Jifeng Feng;

doi: 10.1186/s12859-018-2304-1

pmid: 30075703

pmc: PMC6090782

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

Abstract

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.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.CircPrimer is a user-friendly tool for exploring circRNAs that does not require special user skills.

Related Organizations
Keywords

Genome, Base Sequence, QH301-705.5, RNA Splicing, Computer applications to medicine. Medical informatics, R858-859.7, Molecular Sequence Annotation, RNA, Circular, Sequence, Humans, RNA, Biology (General), Divergent primer, Circular RNAs, Software

  • BIP!
    Impact byBIP!
    citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    		 91
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    		 Top 1%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    		 Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    		 Top 1%
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
91
Top 1%
Top 10%
Top 1%
Green
gold