... | ... | @@ -41,19 +41,27 @@ Within the report of the virulence factors the first columns contain information |
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## Toxins
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For the prediction of toxins in particular two different reports are generated. The first re
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For the prediction of toxins in particular two different reports are generated, a prediction and a library report. Within the prediction report the information on the ORFs (ORF and ORF_ID), are followed by the nr of domain hits (Number_of_hits), the toxin prediction and the prediction of signal peptides. A final Toxin confidence level is given depending on these last two predictions; a confidence level of 1 when a sequence is predicted to contain a toxin domain as well as be secreted, and a level of 2 when only predicted to contain a toxin domain.
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**confidence levels:**
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| Toxin confidence level | HMM prediction | SignalP |
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|:---:| :---:| :---:|
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|1: Secreted Toxin| +| +|
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|2: Non-secreted Toxin| +| - |
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**prediction report:**
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| ORF | ORF_ID | Number_of_hits | Toxin_prediction | Signal_peptide | Toxin_confidence_level |
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|:---:| :---:| :---:| :---:| :---:| :---:|
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| 1_1 | 0000000001 | 2 | pathogenic | Y | 1: Secreted Toxin |
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| 1_2 | 0000000002 | 1 | non_pathogenic | N | - |
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| 2_1 | 0000000003 | 0 | pathogenic | N | 2: Non-secreted Toxin |
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Since the prediction of toxin is based on the presence of identified toxin domains, a second "library" report is generated containing information regarding the identified domains. As well as the ORF ID, the identified domain is reported (HMM_Name) with it's score and significance_evalue, it's full name, the database it is identified with, and a description of the domain.
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**library:**
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| ORF_ID | ORF | HMM_Name | Score | Significance_evalue | NAME | Alternative_name | Database | Description |
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|:---:| :---:| :---:| :---:| :---:| :---:|:---:|:---:|:---:|
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| 0000000001 | 1_1 | PF13091.1 | 34.2 | 1.2e-08 | PLDc_2 | - | PFAM | PLD-like domain
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