Using the T-box riboswitch annotation database
Overview of data table fields (browsable interface)
The T-box riboswitch table contains the following visible fields:
- TBID: T-box riboswitch ID, a unique ID generated by hashing the T-box riboswitch sequence used for the TBDB.
- Host organism: The host organism in which the T-box riboswitch is found.
- Accession number: The accession number of the sequence record in which the T-box riboswitch is present. Clicking on accession number brings users to the corresponding locus.
- Specifier: This is the predicted T-box riboswitch specifier (pairs with tRNA anticodon).
- UGGN: This is the T-box bulge 5'-UGGN-3' sequence that Watson-Crick base pairs with the tRNA 5'-NCCA-3' acceptor arm.
- tRNA: This is the predicted amino acid / tRNA combination that binds the T-box riboswitch.
- Downstream protein: This is the protein encoded by the gene immediately downstream of the T-box riboswitches. Note that some T-box riboswitches (e.g. 01OCB6Q) regulate polycistronic operons; in this case only the first ORF is listed.
Overview of T-box riboswitch entries
Besides the characteristics visible in the main table, more T-box riboswitch data can be found at the subpage for that T-box riboswitch:
- T-box riboswitch source information (ID, host organism, downstream genes, predicted features).
- T-box riboswitch genomic context (NCBI Genome Browser style, showing adjacent genes).
- T-box riboswitch sequence.
- T-box riboswitch secondary structure (dot-bracket notation, as well as an image generated with VARNA).
- Thermodynamic parameters for the predicted secondary structure.
- tRNA ligand predictions from native hosts. Alternative tRNAs are provided if model could not find a consensus. Most likely tRNA is listed as 'Top'.
- Detailed data on the INFERNAL output, for advanced users.
- For translational T-box riboswitch predictions, TBDB output sequence will trim at the end of the antisequestrator stem. The raw input sequence is available in the INFERNAL output module. Note that we currently do not make structural predictions for sequestrator stems.
Quick search on the database
You can search TBDB browser using the search bar provided. Search terms entered will search across all fields.
- Sequence: Show T-box riboswitches which contain your input sequence. Must be DNA, reverse complement strand not searchable.
- Accession: Show T-box riboswitches found within the sequence found at the input genomic accession number.
- Host organism: Show T-box riboswitches from your input species.
- Specifier: Show T-box riboswitches which contain your input specifier sequence. e.g. spec=CUA
- tRNA Family: Show T-box riboswitches which recognize tRNAs for your input amino acid. Predicted from specifier sequence. e.g. Tyr (CUA)
- T-box bulge UGGN: Show T-box riboswitches which contain the desired T-box bulge 5'-UGGN-3' sequence. e.g. UGGN=UCCA
- Amino acid: Show T-box riboswitches that are predicted to sense a specific amino acid. e.g. aa=TYR.
- Found tRNA-pair: Show T-box riboswitches that have had a tRNA pair identified by tRNAscan-SE. e.g. trna=TRUE.
- Downstream protein: Show T-box riboswitches with a particular class of downstream protein. e.g. transporter
- T-box type: Show either translational or transcriptional T-box riboswitches. e.g. translational
- Multiple search parameters: More than one search parameter can be used at a time if delimited by a space. e.g. codon=CUA disc=UCCA bacillus
An advanced search feature is available through the advanced search page.
- Multiple fields can be searched simulatenously by adding more rows using the '+' button.
- Multiple searches will use a strict AND logic, requiring both search terms to be true.
- Only exact matches are allowed.
- Partial matches (i.e. exact match of a portion of an entry) is allowed.
- Search can be reset by using the 'Reset' button.
- To execute search, hit the 'Advanced Search' button.
- Empty fields will be ignored in the search.
Downloading the database
You can download the full database as a csv file from the download page for use offline. Descriptions of each of the fields in the full database can be downloaded from our repository page here
Additionally, the front-end of this site can be downloaded at our site repository here. Note that this only includes the interface for the website, and does not contain the database itself.
Information regarding how the database was built can be found in our BioRxiv publication for the TBDB. Please remember to cite this work if you found it useful.
The pipeline for building the database from raw sequences can be found in our back-end repository.