The Analysis Options wizard screen is the third of five screens used to set up a gene homology alignment. This screen allows you to customize options related to post-assembly analysis.

You can leave all options at their default values or make custom selections, as desired. Each option is described below:

  • Minimum % similarity – The minimum percentage of relatedness between two aligned sequences. Select Automatic to use the default value of 30% or Custom to enter your own value.
  • Minimum % identity – The minimum percentage of bases that must match exactly when any two sequences are aligned. (NCBI definition). Select Automatic to use the default value of 25% or Custom to enter your own value. For example, if you wanted no more than 25 mismatches for a sequence with a length of 500. You would enter 95% (475/500).
  • Minimum % match length – The minimum percent of the gene homolog’s length that must align with the reference. Select Automatic to use the default value of 70% or Custom to enter your own value.
  • Genetic code – Choose from over two dozen genetic codes, including codes from NCBI and DNASTAR Lasergene.

When you are finished making selections on this screen, click Next to proceed to the Assembly Output screen.

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