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RegRNA：一个用于识别调控RNA基序和元件的集成网络服务器。

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.

作者信息

Huang Hsi-Yuan, Chien Chia-Hung, Jen Kuan-Hua, Huang Hsien-Da

机构信息

Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan.

出版信息

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34. doi: 10.1093/nar/gkl333.

DOI:10.1093/nar/gkl333
PMID:16845041
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1538840/
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/.

摘要

众多调控结构基序已被确定在基因表达的转录和转录后调控中发挥着重要作用。RegRNA是一个集成的网络服务器，用于针对输入的mRNA序列识别调控RNA基序和元件的同源物。调控RNA基序的序列同源物和结构同源物均可被识别。RegRNA支持的调控RNA基序分为几类：（i）mRNA 5'非翻译区（5'-UTR）和3'非翻译区中的基序；（ii）参与mRNA剪接的基序；（iii）参与转录调控的基序；（iv）核糖开关；（v）剪接供体/受体位点；（vi）反向重复序列；以及（vii）miRNA靶位点。经过实验验证的调控RNA基序是从文献调研以及几个调控RNA基序数据库中提取的，如UTRdb、TRANSFAC、可变剪接数据库（ASD）和miRBase。整合了多种计算程序用于识别调控RNA基序的同源物。设计了一个直观的用户界面，以促进对用户提交的mRNA序列进行全面注释。RegRNA网络服务器现在可通过http://RegRNA.mbc.NCTU.edu.tw/访问。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/107d/1538840/71d8e46d4b47/gkl333f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/107d/1538840/b5b5cc8780ae/gkl333f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/107d/1538840/71d8e46d4b47/gkl333f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/107d/1538840/b5b5cc8780ae/gkl333f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/107d/1538840/71d8e46d4b47/gkl333f2.jpg

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