sRNATarBase: a comprehensive database of bacterial sRNA targets verified by ezperiments
In bacteria, there exist some small non-coding RNAs (sRNAs) with 40-500 nucleotides in length. Most of them function as posttranscriptional regulation of gene expression through binding to the translation initiation region of their target mRNAs. Therefore, identification and prediction of sRNA targets play an important role in studying sRNA functions.As a first step to acheive the purposes, developing a database for sRNA targets verified by experiments is necessary. For example, it can be used to construct prediction model for sRNA targets.Up to present, there was only one database,sRNAMap, for bacterial sRNA genes and their targets. However, it was mainly developed for sRNAs. There were only 25 sRNA targets. In addition, no web interface for submission of bacterial sRNA targets was provided. Here we present a new database, sRNATarBase, for bacterial sRNA targets. To construct the database, we performed an exhaustive literature search for all experimentally validated sRNA targets. We found 22 relevant papers for E.coiiK12 and 8 papers for salmonella. The total number of targets are 74 for negative regulation and 3 for positive regulation. In addition,no interaction data verified by experiments between sRNA and mRNA are also collected. The number of this kind of targets is 209. The data without intercation is very useful for development of prediction model as negative dataset. For each target, we recorded the bacteria name, sRNA name and sequence, target name and sequence, experimental information,regulation mode (positive, negative, or none),and the paper from which all data were extracted. The database can be accessed at http://ccb.bmi.ac.cn/srnatarbase/.
Yalin Zhao Yuan Cao Xiaomin Ying Lei Cha Ligui Wang Ningsheng Shao Wuju Li
Contribute equally Beijing Institute of Basic Medical Sciences, Taiping Road 27, Haidian district, Beijing 100850, Chin Beijing Institute of Basic Medical Sciences, Taiping Road 27, Haidian district, Beijing 100850, Chin
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
859
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）