Global Alignment Library
This project has been done during my postgrade degree specialising in Bioinformatics (DESS Bioinformatique) at Lille University.
The Project
The goal of this project is to develop a library for global alignment between two genetic sequences. The library is realised in C language. This library is used in another project in JAVA language. The idea is to interface JAVA and C, to have fast programs thanks to C ability. A french version of the project subject is available.
Project parts
The project is composed of two versions:
- The first version of the project is to implement a simple method with a linear gap function, and not a affine gap function. So, opening and extension gap penalties are the same.
- The second version of the project is to implement a method with a affine gap function. So, in this version, opening and extension gap penalties are differents.
Project files
Project files are available here. See the README file for installation information.
This project uses differents sub-directories:
- src, directory with the source files of the project;
- build, directory with the compiled files of the project;
- test, directory with the example files (substitution matrixes, fasta sequences) to test the project;
and differents files, at the project root:
- align(.exe) the project executable file, using alignment algoritm;
- README, a file containing informations about the projet and how to use it;
- TODO, modifications to add to the project;
- Makefile, the file to automized project compilation.
See the README file for installation information.
Project demonstration
Example:
align globalignlinear -10 -2 substitution.matrix query.fasta target.fasta
The result output(missing)
Contact the author:
Pierre MARGUERITE,
Last modified: Tue Mar 22 21:57:22 Romance Standard Time 2005