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
- You are viewing the Oligonucleotide Calculator and Workbook Editor page.
Procedure
- In the Oligonucleotide Workbook Parameters pane, select the Manual Sequence subtab (if necessary).
- 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.
- Chain names can contain up to 250 alphanumeric characters (no symbols).
- You can manually type the chain or copy the chain from a FASTA file using Notepad or another text editing tool.
- 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.
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.
- Select Apply.
- The Results table in the Oligonucleotide Calculator and Workbook Editor updates with results for the new chain added.
- Repeat this process to add additional chains to the oligonucleotide sequence.
Create a .csv file to import sequences to the oligo workbook
Procedure
- In Microsoftâ„¢ Excelâ„¢ (or another spreadsheet application), create a new spreadsheet.
- (Mandatory) Create a "Sequence" column by doing the following:
- In cell A1, type "Sequence" to label the column.
- In the rows below cell A1, type or paste the oligonucleotide sequences you want to add to the oligo workbook.
- You can enter up to 500 sequences.
- 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.
- Each sequence can contain up to 200 bases.
- (Optional) Create a "Name" column by doing the following:
- In cell B1, type "Name" to label the column.
- In the rows below cell B1, enter the name of each entered oligonucleotide sequence.
- Save the spreadsheet as a .csv file.
Use a .csv file to import sequences to the oligo workbook
Prerequisites
- You have created a .csv file containing the oligonucleotide sequences you want to import.
- You are viewing the Oligonucleotide Calculator and Workbook Editor page.
Procedure
- On the command bar of the Oligonucleotide Calculator and Workbook Editor page, select Import Sequence and then select Sequence List (.csv).
- A dialog box opens showing the default file location:
C:\Xcalibur\data
. - You can browse to another folder as necessary.
- Select the .csv file containing the list of sequences you want to import and then select OK.
- The application automatically reads the .csv file and imports the list of sequences into the oligo workbook.
- The Results table in the Oligonucleotide Calculator and Workbook Editor updates with results for the imported sequences.