Bacterial small regulatory RNA databases | Non-coding transcript data analysis
Bacterial sRNAs are a class of small regulatory RNAs of about 40–500 nt in length. They comprise three groups. The first group includes cis-acting sRNAs, which perfectly match their targets with overlapping regions. The second group is comprised of trans-acting sRNAs, which imperfectly match their targets and show separation regions. The third group includes protein-binding sRNAs.
Provides access to information about regulation of transcription initiation of Escherichia coli K-12. RegulonDB is a resource that contains decades of knowledge from classic molecular biology experiments, and from high-throughput genomic methodologies. It provides datasets for interactions for which there is no evidence that they affect expression, as well as expression datasets. A set of tools is also available.
Provides an overview of small RNA (sRNA) in E. coli. ECSBrowser is a comprehensive screening for E. coli sRNAs using a deep sequencing approach. It shows that many as-yet-undiscovered sRNAs are encoded in the E. coli genome. This browser contains the deep sequencing data and detail information about both the novel candidate sRNAs and previously known sRNAs. Furthermore, candidate sRNAs predicted by various methods in the previous studies are also integrated in this browser.
Provides a bacterial sRNA repository. BSRD characterizes sRNA in large-scale transcriptome sequencing projects. This database offers to users functional descriptions for sRNA and contains annotations from manually curated literature mining like groth phase, Hfq binding and Rho-independent terminators. Large-scale target search prediction of identified sRNA is also available, and it includes more than 9000 sRNA entries from up to 900 bacterial strains.
Provides a broad survey of protein coding in bacterial small RNAs (sRNAs). DiSCO-Bac combines summary results, individual open reading frame (ORF) characteristics, and tools for sorting and visualizing genomic context. The database was created by a tool that is based on a flexible machine learning method that employs simple sequence features and comparative genomics. It is able to incorporate a wide range of evidence.
An integrated and comprehensive database comprising plentiful information about small non-coding RNA (sRNA). The sRNAMap provides a variety of interfaces and graphical visualization to present the plentiful information of sRNAs. Users can submit keywords or sequences to search the database. For each sRNA gene, the database provides the sequence, the genomic location, promoter information, secondary structures, literatures, annotations, expression profiles, sequence conservation and its transcriptional regulatory network. Additionally, the sRNAMap has the regulator/sRNA page and the sRNA/target page which provide the experimental conditions and the regulator/sRNA regulations and sRNA/target regulations.
Allows a user-friendly and comprehensive comparative analysis of small non-coding RNAs (sRNAs) from available sequenced gram-positive prokaryotic replicons. Offline versions including analysis and visualization tools facilitate complex user specific bioinformatics analyses. sRNAdb offers biologists an easy access and analysis to both proprietary and public data and allows the identification of a core set of sRNAs which can be used as putative drug targets in antimicrobial therapeutic approaches as well as specific sRNAs for potential diagnostic markers for the detection of gram-positive bacteria.
Gathers information about sequences and functions of transcripts which performs regulatory roles in the cell without protein-coding capacity. ncRNAdb contains about 30 000 sequences from 99 organisms. The database includes both documented RNAs and expressed sequences of Non-Coding RNAs (ncRNAs) with unknown role in cells from several class of transcripts or taxonomic groups. Searches can be made by organism name, RNA symbol or GenBank accession number and a BLAST server to perform sequence similarity searches is provided.