From 6be058c55b247200e4de83b38621bb24061badc0 Mon Sep 17 00:00:00 2001 From: Robert Gifford Date: Thu, 30 May 2024 07:40:58 +0200 Subject: [PATCH] Updated HTML --- md/database-schema.md | 54 ------------------------------ website/user-guide/user-guide.html | 17 ++++++---- 2 files changed, 10 insertions(+), 61 deletions(-) delete mode 100644 md/database-schema.md diff --git a/md/database-schema.md b/md/database-schema.md deleted file mode 100644 index bffcc7a..0000000 --- a/md/database-schema.md +++ /dev/null @@ -1,54 +0,0 @@ -# DIGS screening database field definitions - -When a screen is initiated by the DIGS tool, a project-specific, relational database is created. This 'screening database' captures data generated by DIGS. - -### `searches_performed` table - -Records the details of BLAST searches that have been performed in this DIGS project. - -| **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 | - - -### `digs_results` table - -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. - -| **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 | - diff --git a/website/user-guide/user-guide.html b/website/user-guide/user-guide.html index 24fd889..f35034a 100755 --- a/website/user-guide/user-guide.html +++ b/website/user-guide/user-guide.html @@ -1,14 +1,17 @@ + - - DIGS tool: User Guide - - - - - + + + DIGS: Overview + + + + + +