NOTE

For information about creating mass-only or formula-only oligonucleotide sequences, see Create a mass-only or formula-only oligonucleotide sequence for intact mass analysis.

Procedure

  1. Open the Sequence Manager by selecting Sequence Manager on the BioPharma Finder home page.
  2. Select New Oligonucleotide to the right of the sequence table.
  3. The Oligonucleotide Sequence Editor opens with the Manual Input Sequence pane expanded.
  4. See Oligonucleotide Sequence Editor parameters.
  5. Oligonucleotide Sequence Editor
    Oligonucleotide Sequence Editor

  6. NOTE

    If the resolution or text size of you computer screen is not set properly, you might not be able to see some of the features on the Oligonucleotide Sequence Editor.

    To correct this problem, use the recommended screen resolution of 1920×1080 pixels and consider changing the text size.

  7. To import a FASTA file, select Import FASTA File in the command bar and then browse to the folder containing the FASTA file.
  8. The dialog box displays all of the FASTA files in the selected folder.
  9. The FASTA file must have the ".fasta" extension for the application to be able to find the file.
  10. Select a FASTA file to import, and then select Open.
  11. You can import FASTA files of 1 MB or less.
  12. If a FASTA file contains invalid oligo building blocks or an invalid format, an error message appears. If an error message appears during the import operation, open the FASTA file in a text editor such as Notepad and verify the format of each chain. If the FASTA file contains undefined oligo building blocks, use the Oligo Building Block editor to define them.
  13. The application displays the oligonucleotide sequence information from the FASTA file in the Oligo Sequence Map pane of the Oligonucleotide Sequence Editor.
  14. In addition, the Sequence Information pane displays both the monoisotopic and average masses of the sequence in the Target Oligonucleotide area and the monoisotopic and average masses of the first chain in the Chain area. To view the masses of a different chain, select the chain number from the Chain list.
  15. image/svg+xml Custom 3' terminal Custom 5' terminal Custom base for triplet 2 Custom sugar for triplet 3
    Oligonucleotide Sequence Editor
  16. In the Target Oligonucleotide area, type the name of the sequence and select its category from the Category drop-down list.
  17. See Select the experiment category for a sequence.
  18. Save the new sequence.
  19. See Save an oligonucleotide sequence.
  20. The application adds the saved sequence to the table on the Sequence Manager page.