Options screen

The Options screen is the second wizard screen of the Map Features dialog, and lets you specify mapping options.

• Mapping – Use the text boxes or sliders to specify percent cutoffs for:
  
  
  • Minimum feature coverage, where:
    
    
    
    
  • Minimum sequence identity, where:
    
    
    
    In this calculation, non-common gaps are counted in both source and target sequences.
    
    Feature coverage is less sensitive to insertions and substitutions than is sequence identity. The default for both Mapping items is 80%.

• Translation – The genetic code specified in this dialog is used for translation, as well as for describing the type of sequence change in the Map Features Report file (see next bullet point). By default, MegAlign Pro translates using the genetic code identified in the source data (e.g., the GenBank /transl_table qualifier), if available; otherwise, it uses the standard genetic code (NCBI:1). To specify a different code, check Override genetic code and make a selection from the corresponding drop-down menu. This option does not appear for protein alignments.

• Feature Report – After running the Map Features program, the output is sent to the Map Features Report file. To add a column to that report containing a SeqNinja expression describing the bases in the mapped feature in terms of the source and target sequences, check the box next to Include specific sequence changes.

• Unmapped Interval Report – To make a report listing regions that may need further annotation, check the box next to Generate report of intervals without mapped features. Then use the text box Minimum length of interval to report to specify a minimum length for a stretch of sequence where features were not mapped.

Click Next to proceed to the Output screen.