Amino Acid Explorer

The Amino Acid Explorer is an interactive web-tool that allows users to to quickly vizualize and then explore (in real time) the quantitative relationships between amino acids, both in terms of their biophysical properties, and in terms of the rates and patterns by which they substitute for one another over the course of evolution. It is an analysis tool for the UMBC AAIndex Database, a database of Amino Acid Indices and Amino Acid Similarity Matrices. Specifically, the tool offers three fundamental approaches to exploration:

Explore the similarities and differences of the 20 amino acids of the standard genetic code in terms of their biophysical properties. Example: there are over 100 different published reports of amino acid hydrophobicity. With our tool, you can explore which of these different indices is closest to, or most different from the others, for some or all of the 20 proteinaceous amino acids (How do I Explore Amino Acid Indices?)

Explore the relationship between various biophysical properties of the 20 amino acids of the standard genetic code and an amino acid substitution matrix (such as PAM or BLOSUM) that reflects observed patterns of evolutionary interchange between the amino acids. Example: The BLOSUM62 matrix is the default "scoring matrix" used by BLAST to perform homology searches. What fundamental, quantitative measures of amino acid similarity (e.g. hydrophobicity, size, charge etc.) cause the patterns of interchange recorded in this BLOSUM matrix?

Explore how the observed patterns of amino acid substitution differ in two different substitution matrices, in terms of underlying amino acid biophysical properties. Example: There are over 80 different published amino acid substitution matrices. With our tool, you can explore how BLOSUM62 differs from PAM100 in terms of amino acid charge, size and hydrophobicity

The tool builds on the "spanning-tree" technique described by Tomii et al. (1996)

Run Amino Acid Explorer

System Requirements for using the Amino Acid Explorer

1.	Your browser must have a Java plug-in installed. The tool was tested with JRE version 1.4.2, therefore there is no guarantee that the tool will work with earlier versions. The most up-to-date version of the plugin can be downloaded from http://www.java.com/en/download/manual.jsp

2.	Your browser should allow pop-up windows to be opened by this site. Disabling pop-up windows will prevent help files from appearing.

Note: This product includes software developed by TouchGraph LLC

UMBC AAIndex Database

Note: The UMBC AAIndex Database is a copy of the original AAIndex database. Our local version of the database has been enhanced by making all data available in XML format, allowing easier data exchange with tools that we have developed to explore the AAIndex data.

The UMBC AAIndex Database, implemented by Blazej Bulka, is a database of quantitative properties pertaining to the 20 amino acids of the standard genetic code. Specifically, the database comrpises two different types of data: Amino Acid Indices and Amino Acid Similarity Matrices

The primary purpose of this local implementation was to create an interactive web tool (the Amino Acid Explorer) with which to explore the concept of amino acid similarity. However, we have also built in user-friendly search, browse and download capabilities for the database itself:

For the Amino Acid Indices

(A) Browse all indices

(B) Search for a specific index

For the Amino Acid Similarity Matrices

(A) Browse all matrices

(B) Search for a specific matrix

*(current snapshot of the database generated at the time of the download)

The URL of the UMBC AAIndex Database is

http://www.evolvingcode.net:8080/aaindex/

This material is based upon work supported by the National Science Foundation under Grant No. 0317349.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.