Bengert Peter, Dandekar Thomas
Parasitology, University of Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
Nucleic Acids Res. 2003 Jul 1;31(13):3441-5. doi: 10.1093/nar/gkg568.
We describe an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format. It determines and rapidly scans the different regions of an RNA (including 5' UTR, CDS, 3' UTR in mRNA) and screens for specific RNA signals (in each of these regions, e.g. polyA-site, AU rich region etc. in 3' UTR). It runs a fast folding RNA routine to provide an overview of the RNA fold. Furthermore it analyzes structure content, fold energy and stem loops. In addition, consensus templates are used to determine whether there are any functional structures present for translational control (template: IRE), structured RNA (template: tRNA consensus) or catalytic RNA (template: trans-splicing RNA), giving indications as to how well the structures found match to these templates. The tool box has been implemented as a WWW server at http://wb2x01.biozentrum.uni-wuerzburg.de/.
我们描述了一个用于识别调控RNA元件的综合工具包。RNA分析器收集有关任何以FASTA格式提交的RNA序列或一批序列的一般和特定信息。它确定并快速扫描RNA的不同区域（包括mRNA中的5'UTR、CDS、3'UTR），并筛选特定的RNA信号（在这些区域的每一个中，例如3'UTR中的多聚腺苷酸化位点、富含AU的区域等）。它运行一个快速折叠RNA程序以提供RNA折叠的概述。此外，它还分析结构内容、折叠能量和茎环。此外，共有模板用于确定是否存在用于翻译控制的任何功能结构（模板：IRE）、结构化RNA（模板：tRNA共有序列）或催化RNA（模板：反式剪接RNA），给出所发现的结构与这些模板匹配程度的指示。该工具包已作为一个万维网服务器在http://wb2x01.biozentrum.uni-wuerzburg.de/上实现。
