What DNASTAR software do I need to do antibody phage display analysis?

To do antibody phage display analysis, you’ll need Lasergene Molecular Biology for sequence assembly, sequence alignment and to create phylogenetic trees. If you need structure prediction of the antibody, then NovaFold Antibody and Lasergene Protein are required. Optionally, you can also use NovaDock to simulate docking of antibody to an antigen.

How do I batch translate my antibody sequences?

To batch translate your antibody sequence, use the batch translation template provided in SeqNinja, part of Lasergene Molecular Biology, which will quickly translate the files after trimming.

I have Sanger sequences with vector overhangs. How do I trim my sequences to the right reading frame for translation to protein?

To trim your sequences, first use SeqMan Ultra to assemble the sequences.

Then, show translations by selecting Consensus Translation from the Tracks panel to identify the protein start and stop codons in the antibody.

Finally, manually trim from the 5’ and 3’ ends to remove the vector by selecting and deleting the unwanted sequence.

How do I design primers for this process?

To design primers for antibody phage display, we recommend designing primers that overlap the vector region so you have full antibody sequence coverage for the translation.

How do I align my antibody sequences to create a phylogenetic tree?

To align your antibody sequences, use MegAlign Pro to first perform a multiple sequence alignment and then generate a phylogenetic tree.