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 t...

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Vydáno v:BMC bioinformatics Ročník 23; číslo 1; s. 215 - 8
Hlavní autoři: Zhong, Shanliang, Feng, Jifeng
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 06.06.2022
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Accuracy
Algorithms
Applications software
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer applications
Datasets
Experimental methods
Genetic research
Genetic translation
Genomes
Internal Ribosome Entry Sites
Java (Computer program language)
Life Sciences
Line interfaces
Linux
Microarrays
N6-methyladenosine
Open Reading Frames
Peptides
Protein Biosynthesis
Research methodology
RNA
RNA, Circular
Software
Translation
China
ISSN:1471-2105, 1471-2105
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Shrnutí: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 .
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-022-04705-y