Tutorial: Testcode – An Interactive Analysis

The Gene Inspector is an interactive application. This means that you can perform almost any function at almost any time. It also means that you can interact with some output objects to alter their appearance, rerun an analysis or even continue the analytical process as described in this tutorial for Testcode, and in Tutorial 18: Dot Matrix Analysis – Another Interactive Analysis.

  1. The output from the TestCode analysis can be used to generate additional information or to launch further analyses. This ability is in addition to the ability to recalculate each analysis. Choose Analysis New Analysis… and select the nucleic acid analysis called TestCode.
  2. TestCode is used to determine if an open reading frame is likely to actually code for a protein. The TestCode panel is shown in Figure 39. We will not examine this panel in depth now. The “Minimum Length Open Reading Frame to Consider” should be 200 (labelled `A’ in the figure), the Method should be “Only Stop Codons”, and press the ORFs and rare codons button and choose Drosophila melanogaster as the standard table using the popup menu (labelled `B’ in the figure).
    Figure 39: The TestCode Setup Panel

  3. Click on the Input Sequence icon on the left and choose the sequence hsp70 from the Drosophila Hsps DNA sequence file.
  4. Run the analysis by pressing the Run button. On slower computers, this analysis might take some time to run. While it is running you can enter text into the notebook by clicking in the background and then typing. The Gene Inspector will continue to process analyses while you work in the notebook or even if you switch to a different application. This means that you will never have to interrupt your work while an analysis is running. For time consuming analyses, like database searching or sequence comparisons, this can be a real time saver.
  5. You will get a plot like the one shown in Figure 40. Any points above the upper green threshold line (at about 0.95) correspond to a likelihood of >95% that the region actually codes for a protein. In this case the region from about 1600 to 3600 corresponds to the raised area on the plot and to the open reading frame labelled as `A’. The tick marks indicate the presence of a rare codon. For this predicted protein there are very few rare codons, which also suggests that it is a real gene.
    Figure 40: TestCode Output

  6. The output suggests that the reading frame `A’ codes for a protein and it might be of interest to create a protein sequence corresponding to that region of the DNA. This can be done easily in the Gene Inspector. Double-click on the output object to make it the target.
  7. Now select the ORF of interest by clicking once on the arrow `A’ itself. Once the ORF is selected, choose Object Translate DNA for Selected ORF. The Gene Inspector will read that segment of DNA, translate it using the table you specified in the analysis, and place the generated peptide sequence into a new sequence window.
  8. Click on the name ORF1 in the new sequence window and then choose Sequence Sequence Info…. Note that the program automatically generated appropriate text to help identify the source of the protein.

This is a good example of how the Gene Inspector presents you with intuitive ways of following up on your natural thought process. Once you have examined a DNA sequence for possible coding regions and have identified one, you are likely to want to create a corresponding peptide sequence for further analysis.

This concludes this tutorial. You may quit or continue on to the next tutorial. If you choose to continue, close all open windows now.

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