Metadata-Version: 2.4
Name: pLAST
Version: 1.1.0
Summary: plasmid Language Analysis and Search Tool
Author-email: Kamil Krakowski <k.krakowski@uw.edu.pl>, Stanislaw Dunin-Horkawicz <s.dunin-horkawicz@uw.edu.pl>
License: MIT
Project-URL: Homepage, https://plast.lbs.cent.uw.edu.pl/
Keywords: plasmid,network,language,word2vec,pLAST,model
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: <=3.12,>=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: gensim==4.3.3
Requires-Dist: numba>=0.61.2
Requires-Dist: numpy>=1.26.4
Requires-Dist: pandas>=2.2.3
Requires-Dist: scikit-learn==1.5.2
Dynamic: license-file

![GitHub License](https://img.shields.io/github/license/labstructbioinf/pLAST)
![GitHub repo size](https://img.shields.io/github/repo-size/labstructbioinf/pLAST)
[![Documentation](https://img.shields.io/badge/documentation-blue?logo=github&labelColor=gray)](https://labstructbioinf.github.io/pLAST)
[![pLAST server](https://img.shields.io/badge/pLAST_server-gray?label=pLAST&labelColor=red)](https://plast.lbs.cent.uw.edu.pl/)
[![Figshare data](https://img.shields.io/badge/data-figshare-orange?logo=figshare&labelColor=gray)](https://figshare.com/s/f3e2dfee325b35fdb7d9)
[![PyPI - Version](https://img.shields.io/pypi/v/plast?color=cyan)](https://pypi.org/project/pLAST/)

---

# pLAST

**pLAST** is a computational tool for rapid comparison and classification of plasmid sequences based on their **ORF composition**.

It supports:

- Similarity search against plasmid databases using a single query
- Clustering of large plasmid datasets
- Fast and scalable comparative analysis

---

# 🌐 pLAST Web Interface

The online pLAST server is available here:
👉 [https://plast.lbs.cent.uw.edu.pl/](https://plast.lbs.cent.uw.edu.pl/)

It provides a convenient graphical interface for running searches and visualizing results without installing the software locally.

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# 🛠️ Installation

### Basic installation

pLAST requires Python version 3.9 to 3.12. You can install pLAST directly using:

```bash
pip install plast
```

---

# 🛠️ Full Installation Guide

Detailed installation instructions, including **dependencies**, **environment setup**, and **optional components**, are available in the documentation:
👉 [Installation Documentation](https://labstructbioinf.github.io/pLAST/notebooks/installation.html)

---

# 🧪 Usage Examples

A collection of usage examples demonstrating how to run pLAST, perform searches, and analyze results is available at the following link:
👉 [Usage Examples](https://labstructbioinf.github.io/pLAST/notebooks/usage.html)

These examples provide step-by-step instructions and practical workflows to help you get started quickly.

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# 📊 Data Availability

All datasets used in the project are publicly available on Figshare:
👉 [https://doi.org/10.6084/m9.figshare.30530819](https://doi.org/10.6084/m9.figshare.30530819)
👉 [https://doi.org/10.6084/m9.figshare.30715637](https://doi.org/10.6084/m9.figshare.30715637)

---

# 📚 Documentation

Complete project documentation, including **tutorials**, **examples**, and **API reference**, is available at:
👉 [https://labstructbioinf.github.io/pLAST](https://labstructbioinf.github.io/pLAST)

---

# 📄 Citation

If you use **pLAST** in your research, please cite:

**pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences**
*Kamil Krakowski, Malgorzata Orlowska, Kamil Kaminski, Dariusz Bartosik, Stanislaw Dunin-Horkawicz*
*bioRxiv 2025.11.27.689987; doi: https://doi.org/10.1101/2025.11.27.689987*
