sRNATarBase

RNA Type: small RNA

Overview: sRNATarBase is a database of small regulatory RNA targets in bacterial genomes, obtained by collecting experimental data from literature. There are also two tools: one for the analysis of sRNA-mRNA target interaction in closely related bacterial genomes; and one for sRNA target prediction (sRNATarget - Cao et al, 2009).

Search Methods:

• Similarity: search sequences using the BLAST program. BLAST is also used in conjunction with the tools forPhylogenetic Analysis and Target Prediction.
• Keyword: search by sRNATarBase ID (e.g. SRNAT00001).
• TAG: search by organism, sRNA or Target name, NCBI Code, Target type, regulation, direct or indirect support, PMID.

Source: PubMed and Prediction secondary structure (RNAfold and VARNA).

Information Source: Experimental, Literature, Manual curation.

Information Content: Bacterial, Evidence, Gene, Interaction, mRNA, Phylogeny, Predicted secondary structure, Protein, Regulation, Sequence.

Reference: Cao et al, 2010

PubmedID: 20843985.

Year: 2010

Multiple search: Yes

Download: FASTA, Other.

Genomic Overview: No

Organism: Escherichia coli, Azobacter vinelandii, Bacillus subtilis, Listeria monocytogenes, Neisseria meningitides, Prochlorococcus marinus, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas fluorescens SBW25, Pseudomonas fluorescens strain CHA0, Salmonella enterica subsp. enterica serovar Typhi str. CT18, Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, Staphylococcus aureus subsp. aureus str. NW2, Staphylococcus aureus subsp. aureus str. NEWMAN, Vibrio cholera.

Url: http://ccb.bmi.ac.cn/srnatarbase/