Codon Tools

Amino acid reverse translation and DNA optimization tool based on species-specific codon-use distributions. Species-specifc data can be found on the Codon Usage Database using the NCBI Taxonomy database id (e.g. 413997) or the organism's Latin name (e.g. Escherichia coli B). Mapping species names to Taxonomy IDs can be done here.

Use

$python codon_tools.py --input INPUT_LIST.fasta

To get started, create a conda environment from the environment.yml file.

conda env create -f environment.yml

example contents of INPUT_LIST.fasta:

>SEQ_1
ACDEFGHIKLMNPQRSTVWY
>SEQ_2
ACDEFGHIKLMNPQRSTVWY

Features

1. Reverse translates input amino acid sequence to DNA.
2. Calculates the host's per-AA codon usage profile -- codons used less than a specified threshold (defaults to 10%) are dropped.
3. Compares the reverse-translated DNA sequence to the host profile, determines which codons are overused/underused.
4. Stochastically mutates codons according to host profile.
5. Processes DNA to remove unwanted features:
   • high GC content within a sliding window and across the entire sequence
   • unwanted restriction sites
   • alternate start positions (GA-rich regions 18 bp upstream of ATG/GTG/TTG)
   • 3-consecutive identical codons and 9-mer repeat chunks
   • areas with more than 4 (variable) consecutive identical bps ("local homopolymers")

The process is repeated from step 3 for a specified number of cycles (defaults to 1000) OR until the per-AA codon profile of current DNA and host profile matches (within tolerance).

To do

• remove RNA structure from sequence
• remove predicted splice sites
• store "best" sequence by profile similarity to host and return that to the user