Chimera Evolve

This repository contains the source code for Chimera Evolve, an evolutionary algorithm that designs a single CDS for multiple organisms using the Chimera ARS score.

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Building

The algorithm is written in Rust. After downloading and installing Rust (instructions here), you can generate an executable to run the algorithm as follows:

git clone [email protected]:intbio-ncl/chimera_evolve.git
cd chimera_evolve
cargo build --release

This creates an executable appropriate for your system in chimera_evolve/target/release/. For example, on Linux, from the chimera_evolve directory, you can then run ./target/release/chimera-evolve --help:

David Skelton <[email protected]>
Optimises a single coding sequence for multiple organisms using the Chimera ARS score

USAGE:
    chimera-evolve [OPTIONS] <protein> <cds>... --outfile <outfile>

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -c, --crossovers <crossovers>         Sets the number of crossover events to carry out per generation [default: 100]
    -s, --gen_start <generation_start>    Sets the generation start size. [default: 200]
    -g, --generations <generations>       Sets the number of generations to run the algorithm for [default: 1000]
    -q, --method <method>                 Method to use to score solutions (weighted, min) [default: min]
    -m, --mutations <mutations>           Sets the number of mutation events to carry out per generation [default: 300]
    -o, --outfile <outfile>               Name of the file to which result will be written
    -w, --weights <weights>               Comma separated list of weights if weighted method is used

ARGS:
    <protein>    Sets the protein to optimise a CDS for
    <cds>...     Coding sequences from organisms to optimise for

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Example

The source repository contains some examples to help you get started. To optimise GFP for Bacillus subtilis 168 and Escherichia coli MG1655, after following the steps in the Building section, or moving the pre-compined binaries in the /bin folder, this could be done as follows:

./chimera-evolve \
    examples/proteins/P42212.fasta \ 
    examples/cds/bacillus_subtilis_168.fasta \ 
    examples/cds/escherichia_coli_k12.fasta \
    --outfile optimised.fasta

Or, on Windows (assuming you have the examples folder and chimere-evolve.exe binary in the same folder):

chimera-evolve.exe examples\proteins\P42212.fasta examples\cds\bacillus_subtilis_168.fasta examples\cds\escherichia_coli_k12.fasta --outfile optimised.fasta

This will produce a file called optimized.fasta, which contains the optimised coding sequence and its score.