https://github.com/bibymaths/codonanalyzer
A collection of Perl scripts for analyzing DNA and protein sequences, featuring tools for rare codon detection, GC content profiling, and hydropathy plotting, optimized for Escherichia coli datasets.
https://github.com/bibymaths/codonanalyzer
codon-usage dna-sequences perl protein
Last synced: 3 months ago
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A collection of Perl scripts for analyzing DNA and protein sequences, featuring tools for rare codon detection, GC content profiling, and hydropathy plotting, optimized for Escherichia coli datasets.
- Host: GitHub
- URL: https://github.com/bibymaths/codonanalyzer
- Owner: bibymaths
- License: bsd-3-clause
- Created: 2025-01-18T18:54:52.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2025-05-11T23:17:04.000Z (5 months ago)
- Last Synced: 2025-05-11T23:18:26.379Z (5 months ago)
- Topics: codon-usage, dna-sequences, perl, protein
- Language: Perl
- Homepage:
- Size: 16.1 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# CodonAnalyzer
[](https://snakemake.readthedocs.io)
[](https://doi.org/10.5281/zenodo.15384943)
Originally developed using Perl in 2015, this pipeline has been modernized in 2025 with reproducibility and modularity in mind.
---
## Features
- Codon usage statistics and GC content
- Longest ORF extraction
- Protein sequence translation
- Hydropathy calculation (Kyte–Doolittle)
- Plotting via Python + Matplotlib
- Configurable via `config.yaml`
- Reproducible workflow using Snakemake
---
## Quickstart
```bash
git clone https://github.com/yourusername/codonanalyzer.git
cd codonanalyzer
```
### Setup Environment
```bash
conda install -c conda-forge -c bioconda snakemake matplotlib numpy=1.26.0
```
or using environment.yml:
```bash
conda env create -f environment.yml
```
Then, run:
```bash
snakemake --cores 1
```
---
## Documentation
See the full documentation [here](https://bibymaths.github.io/codonanalyzer).
---
## Author
**Abhinav Mishra**
Email: [mishraabhinav@gmail.com](mailto:mishraabhinav@gmail.com)
For full historical context, see [About](docs/about.md).
---
## License
BSD 3-Clause. See [LICENSE](LICENSE).