Boolean Biotech

Last edit: 08-Mar-18

About

This small project started when I was looking for an implementation of Needleman-Wunsch (pairwise global DNA alignment) in javascript. I just wanted to align two sequences on a website and in a google sheet (using Google Apps Script).

I looked around for a simple javascript implementation (preferably one self-contained javascript file) but I was surprised that I couldn’t find one. Needleman-Wunsch is a pretty simple algorithm so I decided to implement it. I did get a little bit side-tracked…

The first step was to find someone else’s implementation to copy, so I started with some numpy code from @brent_p. Based on his other work, I think it’s a safe assumption it’s implemented correctly. (There is also a complete Cython version in this repo, which implements gap_extend and other parameters, and is obviously much faster. I really just need a very basic alignment so the simpler numpy version is fine for me).

http://blog.booleanbiotech.com/

Tags: DNA
Collection:	project
Start Date:	2014
Status:	active
Type:	Project
Location:	United States

Last edit: 08-Mar-18

About

This small project started when I was looking for an implementation of Needleman-Wunsch (pairwise global DNA alignment) in javascript. I just wanted to align two sequences on a website and in a google sheet (using Google Apps Script).

I looked around for a simple javascript implementation (preferably one self-contained javascript file) but I was surprised that I couldn’t find one. Needleman-Wunsch is a pretty simple algorithm so I decided to implement it. I did get a little bit side-tracked…

The first step was to find someone else’s implementation to copy, so I started with some numpy code from @brent_p. Based on his other work, I think it’s a safe assumption it’s implemented correctly. (There is also a complete Cython version in this repo, which implements gap_extend and other parameters, and is obviously much faster. I really just need a very basic alignment so the simpler numpy version is fine for me).

http://blog.booleanbiotech.com/

Tags: DNA
Collection:	project
Start Date:	2014
Status:	active
Type:	Project
Location:	United States

http://blog.booleanbiotech.com/

Tags: DNA
Collection:	project
Start Date:	2014
Status:	active
Type:	Project
Location:	United States

Last edit: 08-Mar-18

About

This small project started when I was looking for an implementation of Needleman-Wunsch (pairwise global DNA alignment) in javascript. I just wanted to align two sequences on a website and in a google sheet (using Google Apps Script).

I looked around for a simple javascript implementation (preferably one self-contained javascript file) but I was surprised that I couldn’t find one. Needleman-Wunsch is a pretty simple algorithm so I decided to implement it. I did get a little bit side-tracked…

The first step was to find someone else’s implementation to copy, so I started with some numpy code from @brent_p. Based on his other work, I think it’s a safe assumption it’s implemented correctly. (There is also a complete Cython version in this repo, which implements gap_extend and other parameters, and is obviously much faster. I really just need a very basic alignment so the simpler numpy version is fine for me).

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