An efficient locating algorithm for high-frequency biological patterns in genomic sequence

version 0.1 (20240320)

What is it?

Effloc is an efficient locating algorithm for high-frequency biological patterns in genomic sequences.

How to use it?

Effloc consists of three components, index building, pattern generating, and pattern locating. You should first build the FM-index with the reference genome, and then perform the locating process.

Step I. Install

1. Download (or clone) the source code form https://github.com/Lilu-guo/Effloc
2. Compile the source code.

   cd ./Effloc   
   make

Step II. Build FM-index

1. Run the shell command:

   ./effloc <Follow the prompts to enter the genome file name>

Step III. Generate pattern

1. Run the shell command:

   ./effloc <Follow the prompts to enter the pattern set name>

Step IV. Locate pattern

1. Run the shell command:

   ./effloc <Follow the prompts to enter the pattern set name and index file name>

Feedback

Please report bugs to Email: guolilu@stu.xidian.edu.cn or jgxygll@163.com if any questions or suggestions.
Your feedback and test results are welcome.

License

Effloc is available under the MIT license.