Table 3.
Selected other circRNA tools
| Name | Main features | LU | CV | Platform | PL | Link | Ref |
|---|---|---|---|---|---|---|---|
| CircSplice | Alternative splicing | 2019 | — | Unix/Linux | Perl | https://github.com/GeneFeng/CircSplice | [149] |
| CIRI-AS | Alternative splicing | 2018 | v1.2 | Unix/Linux | Perl | https://sourceforge.net/projects/ciri/files/CIRI-AS/ | [147] |
| FUCHS | Alternative splicing | 2018 | Release 0.2.0 | Unix/Linux | Python, R | https://github.com/dieterich-lab/FUCHS/tree/master/GCB_testset | [148] |
| Equivalent-Junctions | Ambiguous splice sites distinguish circRNA and linear splicing | 2019 | — | Unix/Linux | Python | https://github.com/salzmanlab/Equivalent-Junctions | [164] |
| P_RNA_scaffolder | circRNAs assemble | 2019 | — | Unix/Linux | Perl, Shell | https://github.com/CAFS-bioinformatics/P_RNA_scaffolder | [155] |
| CIRI-full | circRNAs assemble | 2018 | v2.0 | Unix/Linux | Java | https://sourceforge.net/projects/ciri-full/ | [45, 151] |
| Sailfish-cir | Expression | 2016 | v0.11 | Unix/Linux | Python | https://github.com/zerodel/Sailfish-cir | [94] |
| IntronPicker | Flanking sequence | 2017 | — | Unix/Linux | Shell | https://github.com/alexandruioanvoda/IntronPicker | [161] |
| ReCirc | Microarrays probe re-annotating program | 2019 | — | Unix/Linux, Windows | R | http://licpathway.net:8080/ReCirc/ | [92] |
| NetMiner | Network (co-expression) | 2017 | v1.0.0 | Unix/Linux | Perl, R | https://github.com/czllab/NetMiner | [145] |
| CircPrimer | Primer Design | 2018 | v1.2 | Windows | Delphi | http://www.bioinf.com.cn/ | [162] |
| CIRCpseudo | Pseudo-gene, circRNA-derived pseudogenes detection | 2017 | — | Unix/Linux | Perl | https://github.com/YangLab/CIRCpseudo | [163] |
| ViennaRNA | Structure | 2019 | v2.4.14 | Unix/Linux, Windows | C++ | https://www.tbi.univie.ac.at/RNA/ | [159, 160] |
| Supernmotifs | Structure | 2017 | v1.2 | Unix/Linux | C++ | http://jpsglouzon.github.io/supernmotifs/ | [156] |
| SpliceV | Visualization | 2019 | — | Unix/Linux | Python | https://github.com/flemingtonlab/SpliceV | [153] |
| CircView | Visualization | 2018 | v1.0 | Unix/Linux, Windows | Java | https://github.com/GeneFeng/CircView | [152] |
| TERate | 4sUDRB-Seq | 2016 | — | Unix/Linux | Shell | https://github.com/YangLab/TERate | [165] |
Header abbreviations: LU, last update; CV, current version; Ref, reference; PL, programming language.
Column descriptions: ‘Name’ is the name of the tool. ‘Main Features’ column describes the key feature of the tool. ‘LU’ column provides the latest update time of the tool. ‘CV’ column describes the current version of the tool. ‘Platform’ column describes the tool supported platforms. ‘PL’ column describes the programming language of the tool. ‘Link’ column provides the homepage link or the link which gives more detailed information about the tool. ‘Ref’ column provides the related publications.