In recent years a new class of small regulatory non-coding RNA (sRNA, ncRNA) was uncovered in addition to the known t- and rRNA classes. These ncRNAs regulate gene expression by different mechanisms and enable bacteria to mount a physiological response due to adaptation to the environment or infection. They range in length from approximately 50 nt to 500 nt and can be subdivided into different types. Riboswitches and cis-regulatory RNAs are part of the mRNA and mainly respond to the availability of nutrients or to abiotic conditions by conformational changes leading to either activation or repression. Furthermore small non-coding transcripts are known to affect the stability and translation of mRNA by cis/trans base pairing to influence regulatory networks in bacteria.
The sRNAdb workbench aims to collect all published and predicted ncRNAs of Gram-positive bacteria and to make them available to the public for comparative analysis. Currently included are all available data of transcriptomic publications on this topic as well as in silico predictions by a software called SIPHT (sRNA identification protocol using high-throughput technologies, http://newbio.cs.wisc.edu/sRNA/). It is implemented with open source components in Java using a client/server model and can be downloaded and installed locally to deal with unpublished data. Optionally the server can be loaded with multiple additional features to assist in the assessment of putative ncRNA loci. Terminators can either be read from the chromosome file (genbank format) or predicted using a software called TranstermHP. Furthermore any data related to the identification of ncRNAs (e.g. promoter boxes, ribosomal binding sites) can be included in sRNAdb based on tab-delimited files. These features are automatically apprehended to the respective services.
A current version of sRNAdb can be downloaded here
and the manual here
Example data can be inserted into each interface using the "example" button.
Search offers a rich query interface for the database resulting in a tabular output. Database fields to retrieve can be selected and filters can be defined to create a specific query. Additional features located in a certain distance up- or downstream of an ncRNA can be appended.
Blast was created to do homology searches of ncRNAs versus either other ncRNAs or whole chromosomes/plasmids using BlastN. Full alignments and concise matrix outputs are both available.
For comprehensive visual assessment the Vision servlet was written, which includes the genomic neighbourhood of ncRNAs in a comparative analysis of multiple related chromosome/plasmid loci. The results are translated into an image (.png) whereby homologue genes (CDS, RNA) are displayed with the same color. Terminators and any number of additional features (e.g. promoters, RBS) which were defined serverside based on tab-delimited flatfiles can be included in the image.