Tjaden Brian
Computer Science Department, Wellesley College, Wellesley, MA 02481, USA.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W109-13. doi: 10.1093/nar/gkn264. Epub 2008 May 13.
Many small RNA (sRNA) genes in bacteria act as posttranscriptional regulators of target messenger RNAs. Here, we present TargetRNA, a web tool for predicting mRNA targets of sRNA action in bacteria. TargetRNA takes as input a genomic sequence that may correspond to an sRNA gene. TargetRNA then uses a dynamic programming algorithm to search each annotated message in a specified genome for mRNAs that evince basepair-binding potential to the input sRNA sequence. Based on the calculated basepair-binding potential of each message with the given sRNA regulator, TargetRNA outputs a ranked list of candidate mRNA targets along with the predicted basepairing interaction of each target to the sRNA. The predictive performance of TargetRNA has been validated experimentally in several bacterial organisms. TargetRNA is freely available at http://snowwhite.wellesley.edu/targetRNA.
细菌中的许多小RNA（sRNA）基因可作为靶信使RNA的转录后调节因子。在此，我们展示了TargetRNA，这是一种用于预测细菌中sRNA作用的mRNA靶标的网络工具。TargetRNA将可能对应于sRNA基因的基因组序列作为输入。然后，TargetRNA使用动态规划算法在指定基因组中的每条注释信息中搜索对输入sRNA序列具有碱基对结合潜力的mRNA。基于计算出的每条信息与给定sRNA调节因子的碱基对结合潜力，TargetRNA输出候选mRNA靶标的排名列表以及每个靶标与sRNA的预测碱基配对相互作用。TargetRNA的预测性能已在几种细菌生物体中通过实验得到验证。可在http://snowwhite.wellesley.edu/targetRNA免费获取TargetRNA。
