preston / alignment

A JavaScript pairwise sequence aligner demonstration using dynamic programming.

Pairwise Sequence Alignment In JavaScript

This is a simple web-based example of how to implement pairwise alignment using dynamic programming techniques. The index.html file uses jQuery and the Bootstrap CSS framework to instantly align two source strings.

You can view a live demo at http://alignment.prestonlee.com.

Legal

Released under the Apache 2 license. Copyright 2014 Preston Lee. All rights reserved.

alignment's Issues

Lack gap opening and gap extension cost

The code can be modified to add gap opening and gap extension cost :

for (var y = curY; y <= rows; y++) { if(trace[y][0] == trace[0][curX] && (trace[y][curX] - (y - curY) * 10) > best) { best = trace[y][curX]; bestX = curX; bestY = y; } } for (var x = curX; x <= cols; x++) { if(trace[curY][0] == trace[0][x] && (trace[curY][x] - (x - curX) * 10) > best) { best = trace[curY][x]; bestX = x; bestY = curY; } }

Name of exact algorithm?

Hello, thanks for great work.

I'm planning to implement an app with sequence alignment and your package looks great!

Can I ask, which algorithm you implements?
(I'm a quite beginner for sequence alignment.)