sequence-alignment-by-cross-correlation 0.1.0
An implementation of sequence alignment on the basis of cross-correlation technique
License: MIT license
Requires Python: >=3.6
Keywords: sequence_alignment_by_cross_correlation

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<h3 align="center">Sequence Alignment<br>by cross correlation</h3>

  <p align="center">
    This is an implementation of the cross correlation algorithm for DNA/RNA alignment
    <br />
    <a href="https://github.com/kuhjuice/sequence_alignment_by_cross_correlation"><strong>Explore the docs »</strong></a>
    <br />
    <br />
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<!-- TABLE OF CONTENTS -->
<details>
  <summary>Table of Contents</summary>
  <ol>
    <li>
      <a href="#about-the-project">About The Project</a>
      <ul>
        <li><a href="#built-with">Built With</a></li>
      </ul>
    </li>
    <li>
      <a href="#getting-started">Getting Started</a>
      <ul>
        <li><a href="#prerequisites">Prerequisites</a></li>
        <li><a href="#installation">Installation</a></li>
      </ul>
    </li>
    <li><a href="#usage">Usage</a></li>
    <li><a href="#roadmap">Roadmap</a></li>
    <li><a href="#contributing">Contributing</a></li>
    <li><a href="#license">License</a></li>
    <li><a href="#contact">Contact</a></li>
    <li><a href="#acknowledgments">Acknowledgments</a></li>
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</details>



<!-- ABOUT THE PROJECT -->
## About The Project
The project is based on the paper [Sequence Alignment by Cross-Correlation](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291754/) and bridges the gap between the knowledge and an useful implementation. The underlying technique is the cross correlation algorithm, which can be tested in this [notebook](https://makeabilitylab.github.io/physcomp/signals/ComparingSignals/index.html).

Another [notebook](https://colab.research.google.com/drive/1XC0AIqli6igxuDt0phcmZCu5IK5tiV7W?usp=sharing) can be seen here. The focus of this notebook is to illustrate how we can use the cross correlation for genomic data.

The gene sequences were obtained using the [NCBI](https://www.ncbi.nlm.nih.gov/gene/) database.

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## Getting Started

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### Prerequisites

This is an example of how to list things you need to use the software and how to install them.
* python3: https://realpython.com/installing-python/

### Installation

1. Clone the repo
   ```sh
   git clone https://github.com/kuhjuice/sequence_alignment_by_cross_correlation.git
   ```
2. Navigate into the repo
   ```sh
   cd sequence_alignment_by_cross_correlation
   ```
3. Install requirements.txt
   ```sh
   pip install -r requirements.txt
   ```
   or
   ```sh
   pip3 install -r requirements.txt
   ```
4. Ask the CLI for help with
   ```sh
   python3 sequence_alignment_by_cross_correlation.py --help
   ```

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<!-- USAGE EXAMPLES -->
## Usage
### Example 1
If we want to get an understanding of what the tool can do for us, we can use the help function of the CLI.
```sh
python3 sequence_alignment_by_cross_correlation/sequence_alignment_by_cross_correlation.py --help
```
![Help Screen Shot][help-screenshot]
### Example 2
If we want to find the gene omcB in the genome of Chlamydia Trachomatis we can use the sequence files in `sequencesToTest`

Executing the following will search for the omcB Gene in the genome of Chlamydia Trachomatis

   ```sh
python3 sequence_alignment_by_cross_correlation/sequence_alignment_by_cross_correlation.py 'sequencesToTest/C_T_genome.fasta' 'sequencesToTest/omcB_C_T_100fit.fna'
   ```

![Usage Screen Shot][usage-screenshot]

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<!-- ROADMAP -->
## Roadmap

- [ ] Fix Bugs
- [ ] Make it a real package
- [ ] Evalueate if useful for other projects

See the [open issues](https://github.com/kuhjuice/sequence_alignment_by_cross_correlation/issues) for a full list of proposed features (and known issues).

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## Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement".
Don't forget to give the project a star! Thanks again!

1. Fork the Project
2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)
3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)
4. Push to the Branch (`git push origin feature/AmazingFeature`)
5. Open a Pull Request

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<!-- LICENSE -->
## License

Distributed under the MIT License. See `LICENSE.txt` for more information.

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<!-- CONTACT -->
## Contact

Bo Kern - [@blood_in_the_water@chaos.social ](https://chaos.social/@blood_in_the_water) - bo@blackscript.de

Project Link: [https://github.com/kuhjuice/sequence_alignment_by_cross_correlation](https://github.com/kuhjuice/sequence_alignment_by_cross_correlation)

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<!-- ACKNOWLEDGMENTS -->
## Acknowledgments

* [TU-Berlin](tu.berlin)
* [Carmen Regner](https://www.tu.berlin/mikrobiologie/ueber-uns/team-personen/#c422452)

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