Note: The classes mentioned in this article are not integrated in the BioJava 1.4 library, yet. However, they are avaiable via CVS.

How do I analyze the symbol properties of an amino acid sequence using the Amino Acid Index database?

To analyze the symbol properties of an amino acid sequence, e.g. the average hydrophobicity of the protein, one can use the interface [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/SymbolPropertyTable.html SymbolPropertyTable]. Its [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/SymbolPropertyTable.html#getDoubleValue(org.biojava.bio.symbol.Symbol) getDoubleValue] method returns a numeric value for a given amino acid symbol, e.g. a negative or positive value that indicates the hydrophobicity of the amino acid relative to the other amino acids. The Amino Acid Index database contains over 500 different amino acid property tables in a simple text file called aaindex1. AAindex1 is also the format name.

This file can be loaded through the AAindexStreamReader class. Afterwards, the property tables can be enumerated by calling the nextTable method, which returns for each property table an AAindex object that implements the SymbolPropertyTable interface. If the file must be hold in memory and random access to the property tables (via the table name) is needed, one can use a SimpleSymbolPropertyTableDB object and initialize it with a AAindexStreamReader object.

The following example shows how to calculate the average hydrophobicity for a given amino acid sequence (in this example the sequence only contains the twenty amino acids) on the basis of the CIDH920105 table from the AAindex1 file aaindex1:

```javaSimpleSymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB(new AAindexStreamReader(new FileReader(“aaindex1”))); AAindex hydrophobicity = (AAindex) db.table(“CIDH920105”); SymbolList symbols = ProteinTools.createProtein(“ARNDCEQGHILKMFPSTWYV”); double hp = 0.0; for (int i = 1; i <= symbols.length(); i++) {

   hp += hydrophobicity.getDoubleValue(symbols.symbolAt(i));

} System.out.println(“Average hydrophobicity: “ + (hp / symbols.length()));```