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 |
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| Hlavní autoři: | , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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BioMed Central
06.06.2022
BioMed Central Ltd Springer Nature B.V BMC |
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| ISSN: | 1471-2105, 1471-2105 |
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| Abstract | 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
. |
|---|---|
| AbstractList | 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.sup.6-methyladenosine (m.sup.6A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m.sup.6A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m.sup.6A 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. 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 . 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.sup.6-methyladenosine (m.sup.6A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m.sup.6A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m.sup.6A sites for circRNAs makes it harder. 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. 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. 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 N6-methyladenosine (m6A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m6A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m6A 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. 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 N6-methyladenosine (m6A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m6A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m6A sites for circRNAs makes it harder.BACKGROUNDSome 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 N6-methyladenosine (m6A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m6A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m6A sites for circRNAs makes it harder.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.RESULTSIn 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.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 .CONCLUSIONScircprimer 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 . 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 -methyladenosine (m A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m A sites for circRNAs makes it harder. 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. 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 . Abstract 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 N6-methyladenosine (m6A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m6A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m6A 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 . |
| ArticleNumber | 215 |
| Audience | Academic |
| Author | Feng, Jifeng Zhong, Shanliang |
| Author_xml | – sequence: 1 givenname: Shanliang surname: Zhong fullname: Zhong, Shanliang organization: Center of Clinical Laboratory Science, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research – sequence: 2 givenname: Jifeng orcidid: 0000-0002-3541-2342 surname: Feng fullname: Feng, Jifeng email: feng_jifeng@sina.com organization: Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/35668371$$D View this record in MEDLINE/PubMed |
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Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner. Internal... Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner. Internal ribosomal... Background Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner. Internal... Abstract Background Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner.... |
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| SubjectTerms | 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 |
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| Title | CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs |
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