NAP How-to Documentation
Comparing a DNA and protein sequence
NAP is simple to use: simply cut-and-paste the DNA sequence into the top box and the protein sequence into the bottom box.Set alignment parameters if desired and click Submit to align.
(Note: The sequence should be a simple text string of 1-letter residue abbreviations only. Do not include FASTA headers or other special characters in the submission or the program will not work properly.)
The program will return a result window showing the alignment in two alternate formats along with statistical information about the alignment parameters and results.
Changing alignment parameters
To alter NAP’s default alignment parameters, choose “External Application Preferences” from the File menu. A window will open allowing you to alter Gap Size, Matrix type, Gap Open penalty, and Gap Extend penalty. When done, click Apply to use these parameters in your NAP session.
Note: Quitting the program and then restarting will not necessarily return parameters to default values. A manual reset is always safest!