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faq.html
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<!doctype html>
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<div class="pt-4">
<h2 class="pt-4">Using the T-box Database</h2>
</div>
<h4>Overview of data table fields (browsable interface)</h4>
<h3>
The T-box table contains the following visible fields:<br> </h3>
<ul id="bulletpoint">
<li>TBID: T-box ID, a unique ID generated by hashing the T-box sequence used for the TBDB.
</li>
<li>Host organism: The host organism in which the T-box is found.
</li>
<li>Accession number: The accession number of the sequence record in which the T-box is present. Clicking on accession number brings users to the corresponding locus.
</li>
<li>Specifier: This is the predicted T-box specifier (pairs with tRNA anticodon).
</li>
<li>T-box: This is the 5'-UGGN-3' sequence that pairs with the tRNA 5'-NCCA-3' acceptor arm.
</li>
<li>Predicted amino acid/tRNA: This is the predicted amino acid / tRNA combination that binds the T-box.
</li>
<li>Downstream protein: This is the protein encoded by the gene immediately downstream of the T-box. Note that some T-boxes (e.g. <a href = "https://tbdb.io/tboxes/01OCB6Q.html">01OCB6Q</a>) regulate polycistronic operons; in this case only the first ORF is listed.
</li>
</ul>
<h4>Overview of T-box entries</h4>
<h3>
Besides the characteristics visible in the main table, more T-box data can be found at the subpage for that T-box:<br></h3>
<ul id="bulletpoint">
<li>T-box source information (ID, host organism, downstream genes, predicted features).
</li>
<li>T-box genomic context (NCBI Genome Browser style, showing adjacent genes).
</li>
<li>T-box sequence.
</li>
<li>T-box secondary structure (dot-bracket notation, as well as an image generated with <a href = "http://varna.lri.fr/">VARNA</a>).
</li>
<li>Thermodynamic parameters for the predicted secondary structure.
</li>
<li>tRNA ligand predictions from native hosts. Alternative tRNAs are provided if model could not find a consensus. Most likely tRNA is listed as 'Top'.
</li>
<li>Detailed data on the INFERNAL output, for advanced users.
</li>
</li>
<li>For translational T-box predictions, TBDB output sequence will trim at the end of the antisequestrator loop. The raw input sequence is available in the INFERNAL output module.
</li>
</ul>
<h4>Quick search on the database</h4>
<h3>
You can search <a href="https://tbdb.io/tbdb.html">TBDB browser</a> using the search bar provided. Search terms entered will search across all fields. <br></h3>
<ul id="bulletpoint"></h3>
<li>Sequence: Show T-boxes which contain your input sequence. Must be DNA, reverse complement strand not searchable.
</li>
<li>Accession: Show T-boxes found within the sequence found at the input genomic accession number.
</li>
<li>Host organism: Show T-boxes from your input species.
</li>
<li>Codon: Show T-boxes which contain your input codon.<i> e.g. codon=CUA</i>
</li>
<li>tRNA Family: Show T-boxes which recognize tRNAs for your input amino acid. Predicted from specifier sequence.<i> e.g. Tyr (CUA)</i>
</li>
<li>Discriminator: Show T-boxes which contain your anti-discriminator base with adjoining anti-acceptor arm.<i> e.g. disc=UCCA</i>
</li>
<li>Amino acid: Show T-boxes that are predicted to sense a specific amino acid. <i> e.g. aa=TYR</i>.
</li>
<li>Found tRNA-pair: Show T-boxes that have had a tRNA pair identified by tRNAscan-SE. <i> e.g. trna=TRUE</i>.
</li>
<li>Downstream protein: Show T-boxes with a particular class of downstream protein. <i> e.g. transporter</i>
</li>
</li>
<li>T-box type: Show either translational or transcriptional T-boxes. <i> e.g. translational</i>
</li>
<li>Multiple search parameters: More than one search parameter can be used at a time if delimited by a space. <i> e.g. codon=CUA disc=UCCA bacillus</i>
</li>
</ul>
</p>
<h4>Advanced search</h4>
<h3>
An advanced search feature is available through the <a href="https://tbdb.io/advanced_search.html">advanced search</a> page.<br></h3>
<ul id="bulletpoint"></h3>
<li>Multiple fields can be searched simulatenously by adding more rows using the '+' button.</li>
<li>Multiple searches will use a strict AND logic, requiring both search terms to be true.</li>
<li>Only exact matches are allowed.</li>
<li>Partial matches (i.e. exact match of a portion of an entry) is allowed.</li>
<li>Search can be reset by using the 'Reset' button.</li>
<li>To execute search, hit the 'Advanced Search' button.</li>
<li>Empty fields will be ignored in the search.</li>
</ul>
<h4>Downloading the database</h4>
<h3>You can download the full database as a csv file from the <a href = "https://tbdb.io/database/tbdb.csv">download page</a> for use offline. Descriptions of each of the fields in the full database can be downloaded from our repository page <a href="https://github.com/mpiersonsmela/tbox/blob/master/Database%20Field%20Description.csv">here</a></h3>
<h3>Additionally, the front-end of this site can be downloaded at our site repository <a href = "https://github.com/jamarchand/tboxdb">here</a>. Note that this only includes the interface for the website, and does not contain the database itself. </h3>
<br>
<h4>Additional information</h4>
<h3>Information regarding how the database was built can be found in our <a href="https://www.biorxiv.org/content/10.1101/2020.06.17.157016v1">BioRxiv</a> publication for the TBDB. Please remember to <a href="https://tbdb.io/citing.html">cite</a> this work if you found it useful.</h3>
<h3>The pipeline for building the database from raw sequences can be found in our <a href="https://github.com/mpiersonsmela/tbox">back-end</a> repository. </h3>
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