The Options screen is the third wizard screen of the Map Features template, and lets you specify the alignment method and other mapping options.

  • In the Align using drop-down menu, choose between the multiple alignment methods Clustal Omega, MAFFT, MUSCLE and Mauve. For more information on each of these algorithms, see this topic of the online MegAlign Pro help.
  • Under Mapping, use the text boxes or sliders to specify percent cutoffs for:

    • Minimum feature coverage, where: feature coverage=(portion of feature contained within the aligned interval)/(feature length) x 100%

    • Minimum sequence identity, where: sequence identity=(number of identical aligned residues)/(length of feature in gapped alignment space) x 100%. 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%.
  • The genetic code is used to create translation annotations for coding sequences. It is also used to characterize variation reported in the report file (see next bullet point). By default, SeqNinja 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.
  • After running the Map Features script, 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.
  • To create an Unmapped Interval 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.

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