Manually create a new oligonucleotide sequence - BioPharma Finder Software - Intact Mass Analysis User Guide - Create oligonucleotide sequences - Manually create a new oligonucleotide sequence - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. On the BioPharma Finder Home page, in the Experiment Types pane, select the Sequence Manager link.
2. The Sequence Manager opens.
2. On the right side of the Sequence Manager, select the New Oligonucleotide button.
3. The Oligonucleotide Sequence Editor opens.

4. 

3. On the left side of the Oligonucleotide Sequence Editor, in the Sequence Information pane > Target Oligonucleotide area, enter the following information:
1. Name: Type the name of the oligonucleotide sequence.
2. Description: (Optional) Type a description for the oligonucleotide sequence.
3. Category: Select the category for the oligonucleotide sequence from the dropdown menu.
4. On the right side of the Oligonucleotide Sequence Editor, expand the Manual Input Sequence pane and then add one chain in the oligonucleotide sequence at a time as follows:
1. Type the name of the chain in the Chain Name box.
2. Type or paste the new chain sequence into the editable box.
3. Select the Apply button.

4. TIP

   Chain names can contain up to 250 alphanumeric characters.

5. NOTE

   You can input oligonucleotide chains using either single-base (ATCGA) or triplet (Ad-pTd-pCd-pAd) notation, using uppercase for bases.

   Both single-base and triplet formats are case-sensitive.

6. TIP

   You can copy and paste the sequence chain from a FASTA file using Notepad or another text editing tool.

7. NOTE

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

   When you copy a chain sequence, do not include these additional comment lines. The application interprets comment lines as sequence building blocks.

8. If the entered chain contains invalid oligo building blocks or an invalid format, an error message appears.
9. The Oligo Sequence Map on the left side of the page updates and displays the added chain.
10. The name of the chain appears above the chain sequence, indicated by a greater-than sign (>) to distinguish each chain.
11. Additionally, the read-only information fields (Monoisotopic Mass, Average Mass, and Formula) in the Sequence Information pane > Target Oligonucleotide area update to reflect the properties of the entire protein.
12. In the Sequence Information pane > Chain area, you can view the Monoisotopic Mass and Average Mass properties for an individual chain by selecting the chain number from the dropdown menu.

13. 

5. Repeat the previous step to add additional chains as needed.

6. 

6. Save the oligonucleotide sequence.
7. The application adds the saved sequence to the Sequence Manager table.