phagetrix 0.1.9

Optimizer for degenerate codon use in phage library generation

Phagetrix

A codon optimizer for phage display library generation.

Example

PhageTrix is a tool to generate phage display libraries. You probably have an idea what AA's you want to replace, and what you wish to replace them with. The sequence companies have a reasonable number of The file format has the AA sequence on the first line. Each following line is the AA to be changed, the digits indicating its position, and the AA options that should be generated for that position. The AA options are concatenated together with no spaces. Phagerix will generate the best degenerate codon for each position.

Example:

VLPYMVAQVQ
P3PFYA
Y4YPFYE
A7AVILM

1. The first line is the sequence you want to alter.
2. The P in position 3 should be either a P, F, Y or an A
3. The Y in position 4 should be either a Y, P, F, or an E
4. The A in position 7 should be either an A, V, I, L or an M

Output:

   1   2   3   4   5   6   7   8   9  10
   V   L   P   Y   M   V   A   Q   V   Q
 GTT CTT BHC BHW ATG GTT DYR CAG GTT CAG

GTTCTTBHCBHWATGGTTDYRCAGGTTCAG

By default this uses the degenerate codons from IDT

Try before buy

Try in Google Colab for free right now: