Manually create a new protein sequence - BioPharma Finder Software - Manually create a new protein sequence - BioPharma Finder Software - BioPharma Finder Software

Procedure

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

4. 

3. In the Chain Name box, type the name of the chain in the new protein sequence.
4. Enter one chain in the sequence at a time by typing or pasting the new chain information into the sequence box.
5. You can manually type the chain or copy the chain from a FASTA file using Notepad or another text editing tool.
6. The name of the chain appears above the chain sequence, indicated by a greater-than sign (>) to distinguish each chain.

7. NOTE

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

   When you copy the chain information, do not include these additional comment lines. The application interprets pasted comment lines as amino acid sequences.

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

8. 

5. Select Apply.
6. If the entered chain contains invalid amino acids or an invalid format, an error message appears.
7. The application displays the protein sequence information from the FASTA file in the Protein Sequence Map pane of the Protein Sequence Editor, with cysteine residues highlighted in yellow for easy visibility.
8. In addition, the Protein Sequence Information pane displays both the monoisotopic and average masses of the sequence in the Target Protein 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.
6. Repeat the steps above to add additional chains to the protein sequence.
7. When you are finished adding chains to your sequence, in the Target Protein area, type the name of the sequence and select its category from the Category drop-down list.
8. See Select the experiment category for a sequence.
8. Save the new sequence.
9. See Save a protein or peptide sequence.
10. The application adds the saved sequence to the table on the Sequence Manager page.