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TestProbe Tutorial

TestProbe basics

  1. Enter your probe in the probe sequence input field.
    A detailed description of the parameters is given when hovering the mouse over the respective area. In this example we pasted a probe sequence and specified the job name, all other parameters were left as default. If you "Use Weighted Mismatches", the type and position of the mismatches will be taken into account (using fractional mismatches).
  2. In the TestProbe Taskmanager you can monitor the progress of all your TestProbe jobs. By selecting a finished TestProbe job in the Task manager you get access to the following options:
    • Share: Generates a link which you can share with others to give them access to your job results.
    • Show result: Opens the result page of the TestProbe job.
    • Show in taxonomy browser: Shows the results in the taxonomy browser (see TestProbe probe evaluation below).
    • Add result to cart: Adds the matched sequences of the submitted probe to your cart.
  3. The 'Table of Top 30 Sequence Matches' is only visible with allowed mismatches or activated 'weighted mismatches' and shows the most frequent types of mismatches. The example below shows results for the alphaproteobacterial probe 'GGTAAGGTTCTGCGCGTT' with "weighted mismatches" enabled. 23023 sequences were matched perfectly. 46 sequences had a mismatch score of 1.1, because the fourth last position was a C and not the expected T (remember that the probe is matched reverse complemented, so the fourth last position of the sequence must be complementary to the fourth position of the probe).
  4. The 'Table of Matched Accessions per Taxonomy' shows the match summaries for each taxonomic group. This data is also visualizable as pie charts in the in the taxonomy browser (see 'TestProbe probe evaluation'). To download the data, just press the "Export To CSV" button.
  5. The 'Table of Matched Regions' shows all sequences that where matched by the submitted probe sequence with detailed match information. To download the data just press the "Export To CSV" button.

TestProbe probe evaluation

  1. TestProbe results can be visually inspected in the Taxonomy Browser (taxonomy drill-down). Click the 'Show in Taxonomy Browser' in the Task manager after selecting the job.
  2. The drop-down menu "Show" in the Taxonomy Browser allows you to switch visualization between TestProbe/TestPrime results. The pie charts shown at the bottom of the Taxonomy Browser change with the taxonomic group selected in the browser. In this example, the genus 'Nevskia' was selected and the pie charts show a coverage of 52.4% for the selected TestProbe result (Nev654).
    Note: Clicking on items in the key will toggle their display. Greyed out items are not displayed (nodata, excluded data).
    Pie charts key:
    •  Left pie chart:
      • match: Matched sequences within the selected taxonomic group.
      • mismatch: Mismatched sequences within the selected taxonomic group.
      • nodata: Sequences that don't have any data in the probe region (not shown in chart by default).
      • excluded data: Sequences that are not covered by the selected database used for inspection of the probe (RefNR for example, not shown in chart by default).
    • Pie chart right:
      • matched ingroup: Matched sequences within the selected group.
      • matched outgroup: Matched sequences outside the selected group.
  3. When inspecting job results in the Taxonomy Browser the cart buttons at the top of every panel adds only the matched sequences to your cart. Hovering over the cart button displays the number of sequences that will be taken into account.
    • The grey percentage provides how many sequences where matched based on all sequences.
    • The green percentage provides how many sequences where matched based on the matchable sequences. This is the probes coverage value.
    • In the below example, the numbers are identical, because all sequences have data in the probe target region (no data 0 (0%)).

ProbeBase Search

  1. Paste a probe sequence or a probe name in the "ProbeBase Search" field and press the search button.
  2. You'll be redirected to the probeBase search page with your results.
  3. On the probes detail page you can click on the SILVA link to get redirected back to the SILVA TestProbe page with the probe sequence automatically pasted in the input field.