Capsular Sequence Typing - Typing Tool Tutorial

One or more (up to 10.000 per run) CST sequences can be pasted (A) or uploaded (B) in Fasta format. It is also possible to submit shorter sequences. When pasting a single sequence the Identifier of the sequence (>Key) should be included (Fasta format). One example sequence is present as a default. A set of three example sequences is also available.

The analysis takes up to a second 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. As soon as the 'Start' button is pushed the results overview is shown. 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, CT and serotype associated with the CT is shown, including the similarity of the sequence. 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 of the typing details per sequence contains a brief overview of the assignment, followed by details such as an alignment of the best matches and a figure of the targeted segment of the wzh gene.