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| # DIGS screening database field definitions | ||
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| When a screen is initiated by the DIGS tool, a project-specific, relational database is created. This 'screening database' captures data generated by DIGS. | ||
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| ### `searches_performed` table | ||
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| Records the details of BLAST searches that have been performed in this DIGS project. | ||
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| | **Field** | **Type** | **Description** | | ||
| |---|---|---| | ||
| | record_ID | INT | Automatically incremented primary key | | ||
| | probe_ID | VARCHAR | Unique iID of probe sequence | | ||
| | probe_name | VARCHAR | Name of probe sequence | | ||
| | probe_gene | VARCHAR | Name of probe sequence gene | | ||
| | target_id | VARCHAR | Unique identifier the TDb file | | ||
| | organism | VARCHAR | Name of the organism (Latin binomial) from which TDb was generated | | ||
| | target_datatype | VARCHAR | Data type of the TDb file | | ||
| | target_version | VARCHAR | Version details of the TDb file | | ||
| | target_name | VARCHAR | Name of TDb file | | ||
| | Timestamp | TIMESTAMP | Timestamp of the table entry | | ||
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| ### `digs_results` table | ||
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| Contains the extracted sequences of the loci specified in BLAST_results table, and results of the second round of paired BLAST, in which extracted sequences are 'genotyped' by BLAST comparison to the reference library. | ||
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| | **Field** | **Type** | **Description** | | ||
| |---|---|---| | ||
| | record_ID | INT | Automatically incremented primary key | | ||
| | organism | VARCHAR | Organism name (Latin binomial) | | ||
| | target_datatype | VARCHAR | Genome data type | | ||
| | target_version | VARCHAR | Genome build version details | | ||
| | target_name | VARCHAR | Name of genome data file containing the BLAST hit | | ||
| | probe_type | VARCHAR | Type of probe sequence (amino acid or nucleotide) | | ||
| | extract_start | INT | 5’ (start) position of reverse BLAST alignment in the RSL sequence | | ||
| | extract_end | INT | 3’ (end) position of reverse BLAST alignment in the RSL sequence | | ||
| | scaffold | VARCHAR | Name of scaffold/contig/chromosome containing the BLAST hit | | ||
| | orientation | ENUM | Orientation of the BLAST hit relative to the probe | | ||
| | assigned_name | VARCHAR | Name of closest matching sequence in RSL | | ||
| | assigned_gene | VARCHAR | Name of gene of closest matching sequence in RSL | | ||
| | bit_score | FLOAT | Bit score of the best match from reverse BLAST | | ||
| | identity | FLOAT | Percentage identity of the best match from reverse BLAST | | ||
| | e_value_num | FLOAT | Coefficient of the expect (e) value for the best match from reverse BLAST | | ||
| | e_value_exp | INT | Exponent (base e) of the expect (e) value for the best match from reverse BLAST | | ||
| | subject_start | INT | 5’ (start) position of reverse BLAST alignment in the RSL sequence | | ||
| | subject_end | INT | 3’ (end) position of reverse BLAST alignment in the RSL sequence | | ||
| | query_start | INT | 5’ (start) position of reverse BLAST alignment in the probe sequence | | ||
| | query_end | INT | 3’ (end) position of reverse BLAST alignment in the probe sequence | | ||
| | mismatches | INT | Number of mismatches in alignment from reverse BLAST | | ||
| | gap_openings | INT | Number of gap openings in alignment from reverse BLAST | | ||
| | sequence_length | INT | Length of the extracted sequence | | ||
| | sequence | TEXT | Text string of the extracted sequence | | ||
| | timestamp | TIMESTAMP | Timestamp of the table entry | | ||
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| <!DOCTYPE html> | ||
| <html lang="en-us"> | ||
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| <head> | ||
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| <meta charset="UTF-8"> | ||
| <title>DIGS: Overview</title> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1"> | ||
| <link rel="stylesheet" type="text/css" href="../assets/stylesheets/normalize.css" media="screen"> | ||
| <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'> | ||
| <link rel="stylesheet" type="text/css" href="../assets/stylesheets/stylesheet.css" media="screen"> | ||
| <link rel="stylesheet" type="text/css" href="../assets/stylesheets/github-light.css" media="screen"> | ||
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| </head> | ||
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| <body> | ||
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| <section class="page-header"> | ||
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| <h1 class="project-name">DIGS</h1> | ||
| <h2 class="project-tagline">Database-Integrated Genome Screening</h2> | ||
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| <a href="../../index.html" class="btn">Home</a> | ||
| <a href="./explore.html" class="btn">Background</a> | ||
| <a href="./user-guide.html" class="btn">Manual</a> | ||
| <a href="https://github.com/giffordlabcvr/DIGS-tool/zipball/master" class="btn">Download</a> | ||
| <a target="_blank" href="https://github.com/giffordlabcvr/DIGS-tool" class="btn">GitHub</a> | ||
| <a target="_blank" href="https://twitter.com/DigsTool" class="btn">Twitter</a> | ||
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| </section> | ||
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| <section class="main-content"> | ||
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| <h3> | ||
| <a id="SearchStructure" class="anchor" href="#SearchStructure" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>Structure of a DIGS-based investigation</strong> | ||
| </h3> | ||
| <hr> | ||
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| <p> | ||
| Comparative studies using database-integrated genome screening (DIGS) entail | ||
| separate 'exploration' and 'analysis' phases, | ||
| with each of these phases being split into two component parts as follows: | ||
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| <ul> | ||
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| <li> <b>Exploration</b>: (1) Setting up and (2) running a similarity search-based screen.</li> | ||
| <li> <b>Analysis</b>: (3) Inspecting screening output via a relational database, and (4) | ||
| performing comparative analysis of exported sequence data.</li> | ||
| </ul> | ||
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| </p> | ||
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| <p><img src="../assets/images/overview-phases.jpg" alt="Overview - phases" /></p> | ||
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| <p> | ||
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| As shown above, this process is usually iterative - at least to some degree - since | ||
| analysis of screening results often reveals new information that can be used to | ||
| design more informative or comprehensive screens. | ||
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| </p> | ||
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| <br> | ||
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| <h3> | ||
| <a id="setUpAndRunScreen" class="anchor" href="#setUpAndRunScreen" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>Exploration phase: Setting up and running an <i>in silico</i> screen</strong> | ||
| </h3> | ||
| <hr> | ||
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| <p> | ||
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| DIGS is a <b>project-based framework</b> in which investigations are centred around | ||
| a <b>genome feature</b> of interest. Any genome feature can be investigated in principle, | ||
| so long as it contains sufficient sequence conservation to be reliably detected in a similarity | ||
| search. | ||
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| </p> | ||
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| <p> | ||
| The '<b>reference sequence library</b>' | ||
| is a curated set of sequences relevant to the genome feature under investigation). | ||
| Usually this will consist of: | ||
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| <ul> | ||
| <li> A set of conserved DNA or polypeptide sequences derived from the genome feature of interest.</li> | ||
| </ul> | ||
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| </p> | ||
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| <p> | ||
| However, depending on the kind of investigation being performed, it may also contain : | ||
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| <ul> | ||
| <li>Sequences that do not derive from the genome feature under investigation, | ||
| but can provide useful information about the locus in which it occurs.</li> | ||
| <li>Sequences representing genome features that are not relevant to the investigation, | ||
| but are sufficiently similar to them to generate 'false positive' matches.</li> | ||
| </ul> | ||
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| Screening entails selecting particular sequences from the reference library for use as | ||
| '<b>probes</b>' in a BLAST search of a specific '<b>target database</b>'. | ||
| </p> | ||
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| <p> | ||
| Sequences that match to the query ('<b>hits</b>') can then be extracted and <b>classified</b>. | ||
| A convenient way of rapidly classifying or 'genotyping' hits is via BLAST-based comparison to the | ||
| reference library, as indicated in the illustration below. | ||
| </p> | ||
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| <p><img src="../assets/images/exploration-phase.jpg" alt="Exploration phase" /></p> | ||
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| <blockquote> | ||
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| <b>Schematic representation of the <u>exploration</u> phase of a DIGS-based investigation</b>. | ||
| <br> | ||
| Here, the genome features being investigated are a set of related genes | ||
| In <b>step (1)</b> a sequence from the reference library is selected and used | ||
| as a 'probe' or 'query' in a BLAST-based search of a chosen target database. | ||
| In <b>step (2)</b>, sequences identified in this search are extracted | ||
| and classified via BLAST-based comparison to the reference library. | ||
| These searches provides a way to effectively 'delve in' to | ||
| genomic databanks and recover related sequences and as such, they provide a means | ||
| to survey unmapped regions of the genomic 'landscape'. | ||
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| </blockquote> | ||
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| <br> | ||
| <h3> | ||
| <a id="analyseScreenOutput" class="anchor" href="#setUpAndRunScreen" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>Analysis phase: Inspecting results and exporting data for comparative analysis</strong> | ||
| </h3> | ||
| <hr> | ||
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| <p> | ||
| In DIGS, a similarity search-based screening pipeline is linked to a <b>relational | ||
| database management system (RDBMS)</b>, and the outputs of screening are captured | ||
| in a <b>project-specific relational database</b>. | ||
| </p> | ||
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| <p> | ||
| This approach not only provides a convenient and robust | ||
| basis for implementing systematic, automated screens that proceed in an efficient, | ||
| non-redundant way, it also allows screening data to be interrogated using | ||
| <b>structured query language (SQL)</b> - a well-established, powerful approach for | ||
| querying relational databases. | ||
| </p> | ||
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| <p> | ||
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| <ol> | ||
| <b> | ||
| <li> Investigation of output via the relational database.</li> | ||
| <li> Comparative genomic analysis of exported sequence data </li> | ||
| </b> | ||
| </ol> | ||
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| <br> | ||
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| <p><img src="../assets/images/analysis-phase.png" alt="Analysis phase" /></p> | ||
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| <blockquote> | ||
| <b>Analysing screening output</b>: A schematic representation of the two component | ||
| parts of the 'analysis' phase of DIGS-based screen | ||
| (some comparative analysis do not require an alignment, but most do). | ||
| </blockquote> | ||
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| <br> | ||
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| <br> | ||
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| <footer class="site-footer"> | ||
| <span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/DIGS-tool">DIGS</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span> | ||
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| <span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong">Jason Long</a>.</span> | ||
| </footer> | ||
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| </section> | ||
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| </body> | ||
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| </html> |
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