An implementation of the basic local alignment search tool (Blast) for nucleotides. The goal of this project is to implement the Blastn algorithm in C++ and interop with an FPGA implementation of the Smith-Waterman algorithm to greatly accelerate the word extension stage of Blastn.
# HTTPS
$ git clone https://github.com/JacobLondon/Blastn.git --recurse-submodules
# SSH
$ git clone [email protected]:/JacobLondon/Blastn.git --recurse-submodules
Run docker build -t blastn . to create the environment with all necessary dependencies. Blastn will be placed under /root.
See the C++ README.md
- Python
- python 3.6+
- pip3
- numpy
- tqdm
- C++
- c++17
- g++ 7.4+
- GNU Make 4.2.1+
Electrical and Computer Engineering Senior Project at California State Polytechnic University, Pomona
- Alden Param
- Alex Chan
- Hmayak Apetyan
- Jacob London
- Simon Tutak
- Sivaramakrishnan Prabakar
- Mostafa M. Hashim Ellabaan
- Mohamed El-Hadedy