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Mise à jour de Alleles of the diphtheria toxin gene authored by Mélanie HENNART's avatar Mélanie HENNART
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Alleles-of-the-diphtheria-toxin-gene.md
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......@@ -2,30 +2,27 @@ _diphtOscan_ identifies the alleles of the _tox_ gene in case of presence of the
A copy of the _tox_ alleles definitions is stored in the [data directory](https://gitlab.pasteur.fr/BEBP/diphtoscan/data) of this repository. The update can be executed with the `-u` option.
## In the "tox_allele" column of the _diphtOscan_ table
## _diphtOscan_ output: "tox_allele" column
Notes:
* _diphtOscan_ tries to report the closest matching allele if a precise match is not found.
* Imprecise allele matches (representing potential novel alleles) are indicated with a `*`.
* _diphtOscan_ will report the allele number of the tox gene, whenever an exact match is found.
* _diphtOscan_ will report the closest matching allele if a precise match is not found; Imprecise allele matches (representing potential novel alleles) are indicated with a `*`.
## In the "TOXIN" column of the *diphtOscan* table
## _diphtOscan_ output: "TOXIN" column
Notes:
* Three references are used as queries for the gene tox: _C. diphtheriae_(), _C. ulcerans_() and _C. pseudotuberculosis_ (). The best query found is noted in the column.
* Annotations indicate aspects of the hit: `*` (inexact identity nucleotide but inexact length coverage).
* For any hit found inexact length coverage from the reference, the mention '_NTTB?' is noted. In addition of 'NTTB': `-X%` (% length of truncated amino acid sequence).
* For further information: `#` (truncated but is a CDS) and `$` (truncated by position at end of contig).
* Three references are used as queries for the tox gene: _C. diphtheriae_(), _C. ulcerans_() and _C. pseudotuberculosis_ (). The best query found will be reported in the column.
* Annotations indicate aspects of the hit: `*` (inexact nucleotide identity but exact length coverage).
* For any hit with inexact length coverage, the mention '_NTTB?' is noted. In addition of 'NTTB': `-X%` (% length corresponding to the missing amino acid sequence).
* Further, additionnal information may be provided: `#` (truncated but is a CDS) and `$` (truncated by position at end of contig).
## Examples
| strain | tox_allele | TOXIN | Interpretation |
|------------|--------------|-----------------------------------|----------------------------------------------------|
| ---------- | ------------ | --------------------------------- | ----------------------------------------- |
| strain A | - | - | tox absent |
| strain B | 1 | tox_diphtheriae | Exact compared to the _C. diphtheriae_ tox reference |
| strain A | 10 | tox_diphtheriae* | Incorrect compared to the reference tox |
| strain B | 2 | tox_diphtheriae;tox_diphtheriae | two copies of tox |
| strain A | 38* | tox_diphtheriae-NTTB?$-20% | Tox is truncated by 20% at the end of the contigs |
| strain B | 24 | tox_diphtheriae-NTTB?-14% | Tox is truncated by 14%. |
| strain B | 6* | tox_ulcerans | Exact compared to the reference tox of _C. ulcerans_ |
| strain A | - | - | the tox gene is absent or less than 50% of its length is detected |
| strain B | 1 | tox_diphtheriae | Exact match compared to the _C. diphtheriae_ tox reference |
| strain C | 10 | tox_diphtheriae* | Inexact match compared to the reference |
| strain D | 2 | tox_diphtheriae;tox_diphtheriae | two copies of tox |
| strain E | 38* | tox_diphtheriae-NTTB?$-20% | tox is truncated by 20% and is located at the end of a contig |
| strain F | 24 | tox_diphtheriae-NTTB?-14% | Tox is truncated by 14% |
| strain G | 6* | tox_ulcerans | Exact match compared to the reference of _C. ulcerans_ |