Tutorial: Customizing and Saving Analysis Setup Suites

You can standardize parameters and set up to run suites of analyses repeated in Gene Inspector.

  1. Select Analysis New Analysis…, choose the Nucleic Acid Analysis button, choose Base Composition, and then press the OK button. Select Dinucleotides from the popup menu and choose to Display results as Number of occurrences. Specify the output type as Graph. Do not run this analysis yet!
  2. Choose Analysis Add Another Analysis… and add Base Distribution. Do a purine distribution by checking just the A and G boxes. Set the parameters to a window of 20 with an offset of 2. Do not run this setup panel yet!
  3. Choose Analysis Add Another Analysis… again and add Restriction Enzyme Digests. Use the Enzyme list popup to choose the Commercial list. Select in the left list all the enzymes starting with the letter `A‘ by selecting AatI, using the scroll bar to scroll down to the last `A’ enzyme (AxyI as of this writing) and then holding down the shift key and selecting this last `A’ enzyme (this is called shift-clicking and is a standard way of extending a selection). Move all the selected enzymes to the right list (of sites to be marked) by pressing the Move>> button.
  4. Select Input Sequences on the left of the analysis setup and add the DNA sequence “bovine LDH” which is in the lactate dehydrogenases DNA file.
  5. This Analysis Setup you have just defined might be something you will use in the future, so let’s add it to the Analysis menu. Choose Analysis Add Setup to Menu… and name the setup “DNA Analysis Suite”. Any time you want to run this set of analyses on a new DNA sequence, you can do so by selecting the DNA Analysis Suite analysis setup from the Analysis menu and then changing the sequences to be analyzed in the input panel.
  6. Run this entire set of analyses by pressing the Run button.
  7. Save the notebook using a name you will remember because you will need it again in Tutorial 15: Restriction Enzyme Digests.

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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  1. […] edition highlights how to save time and facilitate consistency by creating ‘Analysis Suites‘ within Gene Inspector®. Also highlighted is an often overlooked feature in Gene […]

  2. By Gene Inspector® version 2.0 Now Shipping on May 1, 2012 at 4:22 am

    […] has won praise from researchers because it stands alone in allowing biologists to create “suites of analyses” and assign each with a name. This unique feature allows a researcher to setup the analyses […]

  3. […] also discuss how the unique “Analysis Suites” feature offered in Gene Inspector can save a ton of time when investigating new DNA and […]

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