title: RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.
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/.
authors.affiliation: Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan.
authors.forename: Hsi-Yuan
authors.initials: HY
authors.lastname: Huang
authors.forename: Chia-Hung
authors.initials: CH
authors.lastname: Chien
authors.forename: Kuan-Hua
authors.initials: KH
authors.lastname: Jen
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D000818:Animals; D006801:Humans; D020407:Internet; D051379:Mice; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry*; D051381:Rats; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D018511:Systems Integration; D020506:Untranslated Regions / Q000737:chemistry; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid; D020506:Untranslated Regions