Bacterial sRNA data | Non-coding RNA analysis

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A relational database that offers, in an organized and computable form, updated knowledge on transcriptional regulation in Escherichia coli K-12. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Major changes to the overall navigation and structure of the main pages have been made, offering more structured access to the data, based on the two dominant types of users: biologists, usually conducting individual search queries, and those interested in data collections.

Rfam

Provides a collection of noncoding RNA sequences. Rfam is an online resource where RNA sequences are grouped into “families” and “clans” on the basis of nucleotide sequence and secondary structure homology. It includes many different types of ncRNA genes, cisregulatory elements and intronic elements, all annotated in as many species as possible. This database is searched for homologous sequences.

BSRD / Bacterial Small Regulatory RNA Database

(1)

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.

sRNAMap

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.

ECSBrowser / Escherichia coli Small RNA Browser

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.

sRNAdb

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.

DiSCO-Bac / Discovery of sRNA Coding ORFs in Bacteria

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.

PopitschEtAl2017

Provides several informations about antisense and intragenic Small regulatory RNAs (sRNAs). This database allows users to consult data about small RNAs in Borrelia burgdorferi that are important for gene regulation associated with the enzootic cycle of the spirochete. More than 1000 sRNAs are identified in this platform and a large part of them are reported as potentially temperature-dependent.

NPInter / Noncoding RNAs and Protein related biomacromolecules Interaction

Obsolete

Catalogs experimentally determined functional interactions between ncRNAs and proteins, mRNAs or genomic DNA sequences. NPInter integrates the diverse body of experimental knowledge about functional interactions between noncoding RNAs (ncRNAs) (except tRNAs and rRNAs) and protein related biomacromolecules (PRMs) (proteins, mRNAs or genomic DNAs). It sets up a bridge between the coding and noncoding realms.

sRNATarBase

Obsolete

Contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. sRNATarBase 3.0 not only holds the largest number of sRNA-target interactions, but also provides the detailed information regarding sRNA-target binding regions and related mutation experiments. The new version will provide comprehensive support for bacterial sRNA functional studies.

Bacterial small regulatory RNA databases | Non-coding transcript data analysis