Find Resistance
To perform resistance typing, go to:
Microbial Genomics Module (
) | Typing and Epidemiology (beta) (
) | Find Resistance (
)
Select the input genome or contigs (figure 12.1).
Figure 12.1: Pre-assembled and complete- or partial genomes simple contig sequences may be used as input for resistance typing.
You can then specify the settings for the tool (figure 12.2).
Figure 12.2: Select database and settings for resistance typing.
- DB Select the downloaded database for Find Resistance (using the Download of Database for Find Resistance tool (see the Download Database for Find Resistance section).
- Minimum Identity % is the threshold for the minimum percentage of nucleotides that are identical between the best matching resistance gene in the database and the corresponding sequence in the genome.
- Minimum Length % reflect the percentage of the total resistance gene length that a sequence must overlap a resistance gene to count as a hit for that gene. Here represented as a percentage of the total resistance gene length.
- Filter overlaps: will perform extra filtering of results that agree on contig, source and predicted phenotype where one is contained by the other.
The output of the find Resistance tool is a table listing all the possible resistance genes and predicted phenotypes found in the input genome or contigs, as well as additional information such as degrees of similarity between the gene found in the genome and the reference (% identity and query /HSB values), the location where the gene was found (contig name, and position in the contig) as well as a link to NCBI. To add the obtained resistance types to your Result Metadata Table, see the section Add to Result Metadata Table.