RegRNA: an integrated web server for identifying regulatory RNA motifs and elements
Open Access
- 1 July 2006
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 34 (Web Server), W429-W434
- https://doi.org/10.1093/nar/gkl333
Abstract
Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5'-untranslated region (5'-UTR) and 3'-UTR; (ii) motifs involved in mRNA splicing; (iii) motifs involved in transcriptional regulation; (iv) riboswitches; (v) splicing donor/acceptor sites; (vi) inverted repeats; and (vii) miRNA target sites. The experimentally validated regulatory RNA motifs are extracted from literature survey and several regulatory RNA motif databases, such as UTRdb, TRANSFAC, alternative splicing database (ASD) and miRBase. A variety of computational programs are integrated for identifying the homologs of the regulatory RNA motifs. An intuitive user interface is designed to facilitate the comprehensive annotation of user-submitted mRNA sequences. The RegRNA web server is now available at http://RegRNA.mbc.NCTU.edu.tw/.Keywords
This publication has 24 references indexed in Scilit:
- Transterm--extended search facilities and improved integration with other databasesNucleic Acids Research, 2006
- RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elementsNucleic Acids Research, 2005
- Predicting candidate genomic sequences that correspond to synthetic functional RNA motifsNucleic Acids Research, 2005
- UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAsNucleic Acids Research, 2004
- Rfam: annotating non-coding RNAs in complete genomesNucleic Acids Research, 2004
- Riboswitch finder--a tool for identification of riboswitch RNAsNucleic Acids Research, 2004
- Gene regulation by riboswitchesNature Reviews Molecular Cell Biology, 2004
- A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequencesBioinformatics, 2004
- PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequencesNucleic Acids Research, 2003
- Listening to silence and understanding nonsense: exonic mutations that affect splicingNature Reviews Genetics, 2002