Blastn

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.

Project’s New Location

New GitHub

Process

Cloning

# HTTPS
$ git clone https://github.com/JacobLondon/Blastn.git --recurse-submodules

# SSH
$ git clone git@github.com:/JacobLondon/Blastn.git --recurse-submodules

Building and Running

Docker

Run docker build -t blastn . to create the environment with all necessary dependencies. Blastn will be placed under /root.

C++

See the C++ README.md

Dependencies

• Python
  • python 3.6+
  • pip3
  • numpy
  • tqdm
• C++
  • c++17
  • g++ 7.4+
  • GNU Make 4.2.1+

Members

Electrical and Computer Engineering Senior Project at California State Polytechnic University, Pomona

• Alden Param
• Alex Chan
• Hmayak Apetyan
• Jacob London
• Simon Tutak
• Sivaramakrishnan Prabakar

Advisors

• Mostafa M. Hashim Ellabaan
• Mohamed El-Hadedy