Sequence Alignment
by cross correlation

This is an implementation of the cross correlation algorithm for DNA/RNA alignment
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Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Roadmap
5. Contributing
6. License
7. Contact
8. Acknowledgments

About The Project

The project is based on the paper Sequence Alignment by Cross-Correlation 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.

Another notebook 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 database.

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Getting Started

This is an example of how you may give instructions on setting up your project locally. To get a local copy up and running follow these simple example steps.

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 for Users:

1. pip install

 pip install sequence-alignment-by-cross-correlation

2. Use

 python3 -m sequence-alignment-by-cross-correlation.sequence-alignment-by-cross-correlation

Have to figure out how to reduce the amount of string for this module...

Installation for DEVS

1. Clone the repo

   git clone https://github.com/kuhjuice/sequence_alignment_by_cross_correlation.git

2. Navigate into the repo

   cd sequence_alignment_by_cross_correlation

3. Install requirements.txt

   pip install -r requirements.txt

   or

   pip3 install -r requirements.txt

4. Ask the CLI for help

   python3 sequence_alignment_by_cross_correlation.py --help

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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.

python3 sequence_alignment_by_cross_correlation/sequence_alignment_by_cross_correlation.py --help

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

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

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Roadmap

• Fix Bugs
• Make it a real package
• Evalueate if useful for other projects

See the open 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

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

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Contact

Bo Kern - kern@blackscript.de

Project Link: https://github.com/kuhjuice/sequence_alignment_by_cross_correlation

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Acknowledgments

• TU-Berlin
• Carmen Regner

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