General

Allele Typing queries are essentially the same technique as MLST, but are based on whole genome sequence data, and often use a number of targets much larger (e.g. 3000 targets) than basic MLST (using only 7 targets).

This kind of query libraries can additionally have a forth query result state:

  • lin new alleles can be assigned either using the Assign Alleles button in the result for or using the menu action Webupload16.png File | Assign or Submit new Alleles.

Definition Panel

The definition panel is used to define and edit the query. The following fields can be set in the upper part of the panel:

Query Name
A name for this query. This will also be used as category name for the result fields that are filled by this query.
Execution Mode
Perform automatically: Every time the typing is changed, all opened Samples are re-typed.
Never perform automatically: Re-typing has to be started manually using a Sample's context menu.
Comment
A comment for this query. Only shown in the definition panel.

The allele libraries are not managed in the Task Template editor. The command Manage Allele Libraries can be used to manage the libraries.

Result Panel

MLST+ Query Result

The result panel that is a part of the Task Entry overview shows a table where each row represents a target. The columns are:

Target
The target
Source
The source of the sequences, for next-gen data this is the whole-genome-sequencer contig from which the sequence was extracted.
Allele Type
The matching allele type
Query Result
Can have one of the four values: known allele (if the allele was found in library), new allele (if the allele was not found), not done (if the analysis has failed), or no sequence (if no sequence data exists for this target).
Analysis Result
if the analysis has failed this shows the first error that was reported from analysis, otherwise it shows 'OK'.

The toolbar above the table shows the following buttons:

  • Button16-Export.gif Export the table to a file.
  • Button16-Icon file consensus over nav.png Navigate to the contig of the selected target.
  • Button16-SearchSamplesLocally.png Search Samples Locally: Search Samples that use the current Task Template and that have similar allele type combinations in database. Note: the actual DNA sequence of the allele types is not used for similarity calculation. Only the ratio of same allele types and all allele types is used.
  • Button16-AddSTToLibrary.png Assign Alleles: Add new the allele types to the query libraries.