title: sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments.
abstract: Bacterial sRNAs are an emerging class of small regulatory RNAs, 40-500 nt in length, which play a variety of important roles in many biological processes through binding to their mRNA or protein targets. A comprehensive database of experimentally confirmed sRNA targets would be helpful in understanding sRNA functions systematically and provide support for developing prediction models. Here we report on such a database--sRNATarBase. The database holds 138 sRNA-target interactions and 252 noninteraction entries, which were manually collected from peer-reviewed papers. The detailed information for each entry, such as supporting experimental protocols, BLAST-based phylogenetic analysis of sRNA-mRNA target interaction in closely related bacteria, predicted secondary structures for both sRNAs and their targets, and available binding regions, is provided as accurately as possible. This database also provides hyperlinks to other databases including GenBank, SWISS-PROT, and MPIDB. The database is available from the web page http://ccb.bmi.ac.cn/srnatarbase/.
authors.affiliation: Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Cao
authors.forename: Jiayao
authors.initials: J
authors.lastname: Wu
authors.forename: Qian
authors.initials: Q
authors.lastname: Liu
authors.forename: Yalin
authors.initials: Y
authors.lastname: Zhao
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Ying
authors.forename: Lei
authors.initials: L
authors.lastname: Cha
authors.forename: Ligui
authors.initials: L
authors.lastname: Wang
authors.forename: Wuju
authors.initials: W
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D030561:Databases, Nucleic Acid; D016680:Genome, Bacterial; D020407:Internet; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012329:RNA, Bacterial