•If you provided an unannotated template, ArrayStar assumes that the sequences provided are genes/transcripts. You can use the Grouping Sequences as Genes radio buttons to specify whether or not to group sequences as genes, and how to group them.
Note: To enable these options, you must have checked Use sequences as genes if that item was available in the Set Up Preprocessing dialog.
o If there is one sequence per gene, select Don’t group.
o If there are multiple sequences per gene, choose one of the other two options to treat them as alternative transcripts of the same gene. In either case, you must provide a naming convention for grouping the sequences. Automatically group by name uses the full sequence name for the gene. Group by custom regular expression uses a pattern (portion of the sequence name) to group sequences. If you select Group by custom regular expression, you must enter the expression in the text box at right.
•Under Special Gene Handling, check the Exclude pseudogenes box if you wish to exclude features with /pseudo in their annotations.