sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria.
Bacterial sRNAs are a class of small regulatory RNAs of about 40-500 nt in length; they play multiple biological roles through binding to their target mRNAs or proteins. Therefore, elucidating sRNA targets is very important. However, only targets of a few sRNAs have been described. To facilitate sRNA functional studies such as developing sRNA target prediction models, we updated the sRNATarBase database, which was initially developed in 2010. The new version (recently moved to http://ccb1.bmi.ac.cn/srnatarbase/) contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. Among the 771 entries, 475 and 17 were involved in validated sRNA-mRNA and sRNA-protein interactions, respectively, while 279 had no reported interactions. We also presented detailed information for 316 binding regions of sRNA-target mRNA interactions and related mutation experiments, as well as new features, including NCBI sequence viewer, sRNA regulatory network, target prediction-based GO and pathway annotations, and error report system. The new version provides a comprehensive annotation of validated sRNA-target interactions, and will be a useful resource for bacterial sRNA studies.
Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China.
Jiang
J
Wang
Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China.
Tao
T
Liu
Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China.
Bo
B
Zhao
Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China.
Qixuan
Q
Lu
Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China.
Zheng
Z
Wang
Department of Laboratory Medicine, Jinan Military General Hospital, Jinan, Shandong 250031, China labs.net@gmail.com.
Yuan
Y
Cao
Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China wujuchina@126.com.
Wuju
W
Li
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D066289:Data Curation; D030561:Databases, Nucleic Acid; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D023281:Genomics; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics / Q000378:metabolism*
D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated