freqgen 0.1.0

Generate DNA sequences with specified amino acid, codon, and k-mer frequencies.

# Freqgen

<p align =”center”> <img src=’https://raw.githubusercontent.com/Lab41/freqgen/master/logo/Freqgen2-01_icon_only.png’ height=”150”> </p>

[](https://travis-ci.org/Lab41/freqgen) [](https://freqgen.readthedocs.io/en/latest/?badge=latest) [](https://www.codefactor.io/repository/github/lab41/freqgen)

Freqgen is a tool to generate coding DNA sequences with specified amino acid usage frequencies or sequence, GC content, codon usage bias, and/or k-mer usage bias. To accomplish this, Freqgen uses genetic algorithms to efficiently search the solution space of possible DNA sequences to find ones that most closely match the desired parameters.

## Features

• CLI and Python API

• Can simultaneously match multiple DNA statistics

• Built-in visualization utility

• Supports several fitness metrics (and you can bring your own!)

## Installation

Simply run:

$ pip install freqgen

Or, to get the latest (but not necessarily stable) development version:

$ pip install git+https://github.com/Lab41/freqgen.git

## Five-second CLI tutorial

The basic flow of Freqgen can be summarized in three steps:

1. Generate a new amino acid sequence based on the amino acid usage profile of reference sequences. If you already have a specific amino acid sequence in mind (i.e. for synthetic biology uses), skip this step:

$ freqgen aa reference_sequences.fna -o new_sequence.faa -l LENGTH

2. Create a YAML file containing k-mer frequencies for the amino acid sequence’s DNA to have:

$ freqgen featurize reference_sequences.fna -k INT -o reference_freqs.yaml

3. Generate the DNA sequence coding for the amino acid sequence:

   $ freqgen -t reference_freqs.yaml -s new_sequence.faa -v -o optimized.fna

4. Visualize the results of the optimization (optional):

   $ freqgen visualize –target reference_freqs.yaml –optimized optimized.fna

## Documentation

Read the full docs over at [freqgen.readthedocs.io](http://freqgen.readthedocs.io).

## Citation

To be determined!