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)


Chang et al. BMC Bioinformatics 2013 14(Suppl 2):S4   doi:10.1186/1471-2105-14-S2-S4

Open Data