Dengue, Zika & Chikungunya Typing Tool Tutorial

One or more (up to 20000 per run) Arboviruses sequences can be pasted (A) or uploaded (B) in Fasta format (see Fig. 1). Sequences of all regions of the Arboviruses genome can be used.

When pasting a single sequence the Identifier of the sequence (>Sequencename) should be included (Fasta format). One example sequence is present as a default. A set of three example sequences is also available.

The startingpage of the typing tools
Fig. 1. The startingpage of the Dengue Zika & Chikungunya typingtool

The analysis takes up to a few seconds per sequence. Thus, for large batches the run can be viewed later, by typing the Job-Id at C. Here also runs by others can be viewed, if the Job-Id has been communicated. Runs are kept on the server for 1 week.

The startingpage of the typing tools
Fig. 2. Overview of the results

After the 'Start' button is pushed the analysis is started and after a few seconds the results overview is shown (Fig. 2). While the analysis is still in progress the following message is displayed: 'Analysis in progress... (Showing partial results). This page will be automatically updated every 5 seconds...'.

The Job Id number, which can be used to retrieve the results later is displayed at the top of the page as soon as the job is started.
For each sequence the length, positioning on the Dengue genome and assigned genotype are determined.
After the complete analysis is finished the analysis results can be downloaded as XML, CSV or Excel file.
For each sequence more details can be viewed in the individual reports by clicking on 'report' in the results table.

The report contains information on:

  • The sequence submitted (name and length)
  • Blast result: The Arboviruses species of the submitted sequence

No genotype is assigned if:

  • The submitted sequence belongs to another Arboviruses genus. In this case the genus is indicated and the analysis stops.
  • The submitted sequence is shorter than 200 bp. In this case only assignment of the species (Arboviruses) is possible.
  • The bootstrap value < 70. In this case an alignment and a NJ tree are produced which can be used to get an indication of the phylogeny.

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