# Phagetrix
[](https://colab.research.google.com/github/retospect/phagetrix/blob/main/examples/phagetrix.ipynb)
[](https://doi.org/10.5281/zenodo.7676572)
[](https://badge.fury.io/py/phagetrix)
[](https://github.com/retospect/phagetrix/actions/workflows/check.yml)
A codon optimizer for
[phage display library](<https://bio.libretexts.org/Bookshelves/Biochemistry/Supplemental_Modules_(Biochemistry)/4._Biotechnology_2/4.3%3A_M13_Phage_Display_Libraries>)
generation.
When making phage display libraries, it's easy to run out of permutations. 1
liter of phage solution can hold about $10^{12}$ different sequences.
We can approximate how many combinations we generate with
$(nr\ of\ choices)^{(nr\ of\ positions)}$.
If we change the aminoacids to "any" aminoacid, we can change about 9 AA's:
$20^9 \\approx 10^{12}$ permutations.
If we use the degenerate codon capabilities of the manufactureres such as
[IDT](<https://www.idtdna.com/pages/support/faqs/what-are-the-base-degeneracy-codes-that-you-use-(eg.-r-w-k-v-s)->)
to the fullest, we can probably make combinations that are partially rational,
and allow for 6 permutations in any postion.
That allows us to check out many more combinations that are likely to work:
$6^{15} \\approx 10^{12}$, so about 15 variable AA's instead of 9.
This tool allows you to easily specify what AA permutations you want, in which
position, and calculates the best sequence of degenerate codons.
## 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 want 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.
Phagetrix will generate the best degenerate codon for each position.
Example:
```txt
VLAYMVAQVQ
A3AGVIL
Y4YFW
A7AVIL
```
1. The first line is the sequence you want to alter.
1. The P in position 3 should be either a P, F, Y or an A
1. The Y in position 4 should be either a Y, P, F, or an E
1. The A in position 7 should be either an A, V, I, L or an M
Output:
```txt
phagetrix ./sample.phagetrix
1 2 3 4 5 6 7 8 9 10
V L A Y M V A Q V Q
GTT CTT VBA TDK ATG GTT VYA CAG GTT CAG degenerate codons
56 50 67 percentage on target
1V 1L 1V 1Y 1M 1V 1V 1Q 1V 1Q
1L 1W 1L
1I 1F 1I
1G -- 1A
1A 1L --
-- 1C 1T
2R 1* 1P
1T
1P
GTTCTTVBATDKATGGTTVYACAGGTTCAG
```
The lines of the output show:
1. number of the AA on the first line
1. original AA on the second line
1. codon made from degenerate basepairs
1. the percentage of product for this codon that matches what the user specified
1. how many codons code for which aminoacid. The AA below the `--` line are
off-target codons that were not requested.
- the last line shows the codons made from degenerate basepairs again, in a
format that can easily be copied and pasted.
By default this uses the degenerate codons from
[IDT](<https://www.idtdna.com/pages/support/faqs/what-are-the-base-degeneracy-codes-that-you-use-(eg.-r-w-k-v-s)->).
## Additional features
Adding a comment of this form to your input file (see the pal.phagetrix file in
the example directory)
```txt
# offset = 20
```
allow the setting of variables - in this case, the first aminoacid will be
numbered 21. This is nice for long sequences where "something in the middle"
needs to be edited.
# Try it
- [](https://colab.research.google.com/github/retospect/phagetrix/blob/main/examples/phagetrix.ipynb)
- Install it on your machine `pip install phagetrix` to get the `phagetrix`
command line tool. Requires python3.
# Related projects
Other projects that are potentially interesting, if you are into this sort of
stuff.
- [Make primers for highly variable genomes](https://github.com/jonas-fuchs/varVAMP)
Raw data
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