You can manually add oligonucleotide sequences to the oligo workbook one sequence at a time or use the Import Sequence function to add up to 500 sequences at a time using a specifically-formatted .csv file.

Manually add sequences to the oligo workbook

Prerequisites

  1. You are viewing the Oligonucleotide Calculator and Workbook Editor page.

Procedure

  1. In the Oligonucleotide Workbook Parameters pane, select the Manual Sequence subtab (if necessary).
  2. Add one chain in the oligonucleotide sequence at a time by typing the name of the chain in the Chain Name box and then typing or pasting the new chain sequence into the sequence box.
  3. Adding oligonucleotide sequences to the oligo workbook manually
    Adding oligonucleotide sequences to the oligo workbook manually
  4. Chain names can contain up to 250 alphanumeric characters (no symbols).
  5. You can manually type the chain or copy the chain from a FASTA file using Notepad or another text editing tool.
  6. You can input the chains into the sequence box 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.
  7. 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.

  8. Select Apply.
  9. The Results table in the Oligonucleotide Calculator and Workbook Editor updates with results for the new chain added.
  10. Repeat this process to add additional chains to the oligonucleotide sequence.

Create a .csv file to import sequences to the oligo workbook

Procedure

  1. In Microsoftâ„¢ Excelâ„¢ (or another spreadsheet application), create a new spreadsheet.
  2. (Mandatory) Create a "Sequence" column by doing the following:
  3. In cell A1, type "Sequence" to label the column.
  4. In the rows below cell A1, type or paste the oligonucleotide sequences you want to add to the oligo workbook.
  5. You can enter up to 500 sequences.
  6. 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.
  7. Each sequence can contain up to 200 bases.
  8. (Optional) Create a "Name" column by doing the following:
  9. In cell B1, type "Name" to label the column.
  10. In the rows below cell B1, enter the name of each entered oligonucleotide sequence.
  11. Creating a .csv file to import sequences to an oligo workbook
    Creating a .csv file to import sequences to an oligo workbook
  12. Save the spreadsheet as a .csv file.

Use a .csv file to import sequences to the oligo workbook

Prerequisites

  1. You have created a .csv file containing the oligonucleotide sequences you want to import.
  2. You are viewing the Oligonucleotide Calculator and Workbook Editor page.

Procedure

  1. On the command bar of the Oligonucleotide Calculator and Workbook Editor page, select Import Sequence and then select Sequence List (.csv).
  2. A dialog box opens showing the default file location: C:\Xcalibur\data.
  3. You can browse to another folder as necessary.
  4. Select the .csv file containing the list of sequences you want to import and then select OK.
  5. The application automatically reads the .csv file and imports the list of sequences into the oligo workbook.
  6. The Results table in the Oligonucleotide Calculator and Workbook Editor updates with results for the imported sequences.
  7. Results table in the Oligonucleotide Workbook and Calculator Editor updated with imported oligonucleotide sequences
    Results table in the Oligonucleotide Workbook and Calculator Editor updated with imported oligonucleotide sequences