Skip to content

The Blastn (Basic Local Alignment Search Tool for Nucleotides) algorithm with Smith-Waterman scoring implemented for FPGAs

License

Notifications You must be signed in to change notification settings

JacobLondon/Blastn

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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

Blastn 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

About

The Blastn (Basic Local Alignment Search Tool for Nucleotides) algorithm with Smith-Waterman scoring implemented for FPGAs

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Contributors 4

  •  
  •  
  •  
  •