This is continued from Part A: Create a templated assembly in SeqMan NGen.

If your assembly has a large number of variants, you can use ArrayStar to filter them down to a smaller group of interest before sending them to SeqMan Pro for viewing. This optional step is highly recommended for all but very small assemblies.

  1. Launch ArrayStar and choose Open a project.

  1. Navigate to and select the .astar file output by SeqMan NGen.
  1. When the file has loaded, click on the SNP Table tab.
  1. Use Filter > Filter All to perform any desired filtering.

  1. At the conclusion of filtering, click the Remember Results as a Variant Set tool () above the Search Results table. Type in any desired name and press OK.

  1. In the Action section in the center-right of the window, click the link Select and show the table of this set’s Variants.
  1. Use the Choose Quick-Filter drop-down to select Show Only Variant Set.

In the ensuing dialog box, select the named set and click OK.

  1. Click on Add/Manage Columns. Select SeqMan NGen Assembly Variants, then pdbID. Click Add Column and OK.
  1. In the SNP Table, click on the pdbID column header to sort the column and locate rows with PDB entries.
  1. Within the subset of rows with PDB entries, select any row of interest. Then right-click on it and choose Send Selection to SeqMan Pro.

  1. If prompted, select an individual sample of interest and press OK.

Continue to Part C: View variants in SeqMan Pro.

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