Global and Local Sequence Alignment Algorithms

Initializing live version
Download to Desktop

Requires a Wolfram Notebook System

Interact on desktop, mobile and cloud with the free Wolfram Player or other Wolfram Language products.

Sequence alignment is widely used in molecular biology to find similar DNA or protein sequences. These algorithms generally fall into two categories: global, which align the entire sequence, and local, which only look for highly similar subsequences. This Demonstration uses the Needleman–Wunsch (global) and Smith–Waterman (local) algorithms to align random English words. Gaps are shaded yellow, mismatches orange, and matches red (with a lighter shade for those matches not appearing in the final alignment).

Contributed by: Jordi Silvestre-Ryan (March 2011)
Open content licensed under CC BY-NC-SA



This Demonstration uses a simple gap penalty, in which each insertion or deletion is scored the same. Because large gaps occur frequently in biological sequences, it is often better to use an affine gap penalty, which uses different values for opening and extending a gap.

For a technical description of the algorithms used, please see the following references:

N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, Cambridge, MA: The MIT Press, 2004.

I. Korf, M. Yandell, and J. Bedell, BLAST, Sebastopol, CA: O'Reilly & Associates Inc., 2003.

Feedback (field required)
Email (field required) Name
Occupation Organization
Note: Your message & contact information may be shared with the author of any specific Demonstration for which you give feedback.