Class AAindexStreamReader

  • All Implemented Interfaces:

    public class AAindexStreamReader
    extends Object
    implements SymbolPropertyTableIterator
    Iterator over AAindex objects that are stored in a stream in the AAindex1 file format. The format of such an Amino Acid Index Database file is described in the AAindex manual . The nextTable() method returns objects of type AAindex. See this class also for further informations. To hold an AAindex1 file in memory for random access use the SimpleSymbolPropertyTableDB class:
     SimpleSymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB(
             new AAindexStreamReader(new FileReader("aaindex1")));
     AAindex hydrophobicity = (AAindex) db.table("CIDH920105");
     SymbolList symbols = ProteinTools.createProtein(
     double hp = 0.0;
     for (int i = 1; i <= symbols.length(); i++) {
         hp += hydrophobicity.getDoubleValue(symbols.symbolAt(i));
     System.out.println("Average hydrophobicity: " + Double.toString(
             hp / symbols.length()));


    AAindex web site.

    Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000).

    Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996).

    Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988)

    Martin Szugat