CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs

BACKGROUND: Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner. Internal ribosomal entry site (IRES) and N(6)-methyladenosine (m(6)A) were reported to drive translation of circRNAs. Experimental methods confirming...

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Autores principales: Zhong, Shanliang, Feng, Jifeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9169404/
https://www.ncbi.nlm.nih.gov/pubmed/35668371
http://dx.doi.org/10.1186/s12859-022-04705-y
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author Zhong, Shanliang
Feng, Jifeng
author_facet Zhong, Shanliang
Feng, Jifeng
author_sort Zhong, Shanliang
collection PubMed
description BACKGROUND: Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner. Internal ribosomal entry site (IRES) and N(6)-methyladenosine (m(6)A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m(6)A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m(6)A sites for circRNAs makes it harder. RESULTS: In this report, we present circPrimer 2.0, a Java based software for annotating circRNAs and predicting ORFs, IRESs, and m6A sites of circRNAs. circPrimer 2.0 has a graphical and a command-line interface that enables the tool to be embed into an analysis pipeline. CONCLUSIONS: circprimer 2.0 is an easy-to-use software for annotating circRNAs and predicting translation potential of circRNAs, and freely available at www.bio-inf.cn. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04705-y.
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spelling pubmed-91694042022-06-07 CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs Zhong, Shanliang Feng, Jifeng BMC Bioinformatics Software BACKGROUND: Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner. Internal ribosomal entry site (IRES) and N(6)-methyladenosine (m(6)A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m(6)A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m(6)A sites for circRNAs makes it harder. RESULTS: In this report, we present circPrimer 2.0, a Java based software for annotating circRNAs and predicting ORFs, IRESs, and m6A sites of circRNAs. circPrimer 2.0 has a graphical and a command-line interface that enables the tool to be embed into an analysis pipeline. CONCLUSIONS: circprimer 2.0 is an easy-to-use software for annotating circRNAs and predicting translation potential of circRNAs, and freely available at www.bio-inf.cn. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04705-y. BioMed Central 2022-06-06 /pmc/articles/PMC9169404/ /pubmed/35668371 http://dx.doi.org/10.1186/s12859-022-04705-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Zhong, Shanliang
Feng, Jifeng
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
title CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
title_full CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
title_fullStr CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
title_full_unstemmed CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
title_short CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
title_sort circprimer 2.0: a software for annotating circrnas and predicting translation potential of circrnas
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9169404/
https://www.ncbi.nlm.nih.gov/pubmed/35668371
http://dx.doi.org/10.1186/s12859-022-04705-y
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AT fengjifeng circprimer20asoftwareforannotatingcircrnasandpredictingtranslationpotentialofcircrnas

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