‒ an integrated web server for identifying functional RNA motifs and sites
Home Scan Statistics Documentation Tutorial Release 2.0, Jun. 2012

  System Architecture

We developed an integrated web server, namely RegRNA 2.0, to comprehensively identify homologs of functional RNA motifs and sites in an RNA sequence. Various analytical approaches and data sources were incorporated into RegRNA 2.0. Through our easy-to-use web server, user can conveniently use these programs without having to download the code and get the programs to run. The predictive results and related information are presented with good graphical visualization on RegRNA 2.0 web page. The research components of RegRNA 2.0 are shown as figure below :


   Comparison

As compared with RegRNA, RegRNA 2.0 integrates more data and is capable of identifying more types of functional RNA motifs (as shown in Table below). In addition, RegRNA 2.0 provides further analysis and related information for predictive results, and presents results with good graphical visualization.

Features

RegRNA

RegRNA 2.0

Polyadenylation sites

none

Yes (polya_svm)

Ribosome binding sites

none

Yes (RBSfinder)

Rho-independent terminator

none

Yes (TransTermHP)

RNA editing sites

none

Yes (CURE)

AU-rich elements

none

Yes (ARED 5 patterns)

RNA cis-elements

none

Yes (Rfam & ERPIN 220 cis-elements)

Similar functional RNAs

none

Yes (BLAST+fRNAdb 475,318 fRNAs)

ncRNA hybridization region

none

Yes (BLAST+RNAcofold+NONCODE 170,581 ncRNAs)

Open reading frame

none

Yes (RegRNA 2.0 program)

Motif region structure

none

Yes (RNAfold)

RNALogo displaying

none

Yes (RNALogo)

GC-content Ratio

none

Yes (RegRNA 2.0 program)

RNA accessibility

none

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 descriptor)

Yes & Updated (RiboSW, Rfam models)

miRNA target sites

Yes (miRBase 744 miRNAs)

Yes & Updated (miRBase 21,643 miRNAs)

Splicing sites

Yes (GeneSplicer)

Yes (GeneSplicer)

Long stems

Yes (EMBOSS einverted)

Yes (EMBOSS einverted)

User defined Motifs

Yes (RNAMotif)

Yes (RNAMotif)


   References

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