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. Manual Input Sequence pane
    Manual Input Sequence pane
  6. In the Chain Name box, type the name of the chain in the new oligonucleotide sequence.
  7. Under the Chain Name box, enter one chain in the sequence at a time by typing or pasting the new chain information into the sequence box.
  8. You can manually type the chain or copy the chain from a FASTA file using Notepad or another text editing tool.
  9. You can input the chains using either single-base (plain) notation (ATCGA) or triplet notation (Ad-pTd-pCd-pAd), using upper case for bases. Both single-base and triplet formats are case-sensitive.
  10. The name of the chain appears above the chain sequence, indicated by a greater-than sign (>) to distinguish each chain.

  11. NOTE

    The FASTA file might contain comment lines that begin with a greater-than sign (>), similar to the chain name.

    When you copy the chain information, do not include these additional comment lines. The application interprets pasted comment lines as oligo building blocks.

    Only the chain name entered in the Chain Name box should appear as a comment line (>) in the sequence box.

  12. Select Apply.
  13. If the entered chain contains invalid oligo building blocks or an invalid format, an error message appears.
  14. The application displays the oligonucleotide sequence information from the FASTA file in the Oligo Sequence Map pane of the Oligonucleotide Sequence Editor.
  15. 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.
  16. Oligo Sequence Map
    Oligo Sequence Map
  17. Repeat this process to add additional chains to the oligonucleotide sequence.
  18. When you are finished adding chains to your sequence, in the Target Oligonucleotide area, type the name of the sequence and select its category from the Category drop-down list.
  19. See Select the experiment category for a sequence.
  20. Save the new sequence.
  21. See Save an oligonucleotide sequence.
  22. The application adds the saved sequence to the table on the Sequence Manager page.