Table 2 A comparison between RegRNA 2.0 and RegRNA
Features | RegRNA[27] | RegRNA 2.0 |
|---|---|---|
Polyadenylation sites | - | Yes (polya_svm) |
Ribosome binding sites | - | Yes (RBSfinder) |
Rho-independent terminator | - | Yes (TransTermHP) |
RNA editing sites | - | Yes (CURE) |
AU-rich elements | - | Yes (ARED) |
RNA cis-elements | - | Yes (Rfam & ERPIN) |
similar functional RNAs | - | Yes (BLAST+fRNAdb) |
ncRNA hybridization region | - | Yes (BLAST+RNAcofold+NONCODE) |
Open reading frame | - | Yes (RegRNA 2.0) |
Motif region structure | - | Yes (RNAfold) |
RNALogo displaying | - | Yes (RNALogo) |
GC-content Ratio | - | Yes (RegRNA 2.0) |
RNA accessibility | - | Yes (RNAplfold) |
DNA motifs | Yes (TRANSFAC 7.4) | Yes & Updated (TRANSFAC 2012.1) |
Splicing regulatory motifs | Yes (AEDB 278 motifs) | Yes & Updated (AEDB 294 motifs) |
UTR motifs | Yes (UTRSite 40 motifs) | Yes & Updated (UTRSite 48 motifs) |
Riboswitches | Yes (RNAMotif) | Yes & Updated (RiboSW & Rfam) |
miRNA target sites | Yes (744 miRNAs) | Yes & Updated (miRBase 21,643 miRNAs) |
Splicing sites | Yes | Yes (GeneSplicer) |
Long stems | Yes | Yes (EMBOSS einverted) |
User-defined Motifs | Yes | Yes (RNAMotif) |