Team:Stanford-Brown/Software
We created a software program for automated protein optimization and gibson assembly primer design. When supplied a list of DNA or amino acid sequences representing proteins, the program will not only codon optimize the sequence for a user-defined species, but also remove any common restriction sites from the sequence. The program can also process multiple sequences, allowing the user to process a large number of sequences quickly and identifying which sequences have issues. Under the gibson assembly primer module, our program accepts a list of fragments to be stitched together, calculates the homology needed to gibson the fragments together, and designs primers for fragment homology PCR extension matching a user-defined melting temperature. These optimized protein DNA sequences or Gibson primers are then provided to the user in a text file. For ease of use, our program also reports errors and procedures in terminal and the output file. To see this work, please go to our software page here.
