Isolate-scheme dependencies and the sequence type
An isolate (as shown in figure 4.4) is created by defining a scheme to use as a reference. The scheme is used to:
- Automatically assign sequences to loci (see Assemble and create isolate).
- Determine the allele type for the consensus sequence for each locus (at the top of the isolate view).
- Determine the sequence type of the isolate.
For each locus, the Multilocus Sequence Typing Module compares the reference sequence of the isolate's contig with all the allelic types in the scheme. If there is a perfect match, an allelic type is assigned. If not, the allele type will be "New allele" (in this case, the new allele can be compared to the nearest allele in the scheme, see Align to nearest allele).
The sequence type is shown in the field at the middle of the view and determined by the Multilocus Sequence Typing Module by comparing the allelic profile (all the allele types) of the isolate with the allelic profiles in the scheme (see Profile table).
If none of the allelic profiles are identical to the isolate's allelic profile, the text field will say: "New type". If there are one or more loci where no sequences have been assigned, there could be a number of possible sequence types because one or more allelic type is unknown. All the possible sequence types will then be listed.
The isolate is dynamically linked to the scheme, meaning that if the scheme is updated, the allelic types and the sequence type of the isolate is calculated again. In this case, a dialog is presented to inform you that the information in the isolate view is about to change.
If you wish to use another scheme as basis for typing the isolate,
click the Browse button (
) next to the scheme name at
the bottom of the view.
Clicking Find in Navigation Area (
) will
select the scheme that is currently used for typing the isolate.