Representation of amino acid sequences as two-dimensional point patterns.
An algorithm for the representation of amino acid sequences as two-dimensional point patterns (2-D plot) is described. The algorithm is based on chaos game representation (CGR) for DNA sequences and was extended for amino acid sequences. The 2-D plot depicts the sequentiality of amino acids and the amino acid composition of a protein. Changes in a protein sequence as insertion, deletion and repeats of amino acids are characterized by specific geometrical properties and changes in the 2-D plots. The 2-D plot may be considered as a two-dimensional "fingerprint" of a protein. The properties of the algorithm are explained by user-defined amino acid sequences. As an example the 2-D plots of two selected heart proteins are generated. The sequences of these proteins are obtained from the protein sequence database SWISS-PROT.
Pleissner
K P
KP
Department of Internal Medicine/Cardiology, Virchow-Klinikum of the Humboldt University and German Heart Institute Berlin. pleiss@dhzb.de
Wernisch
L
L
Oswald
H
H
Fleck
E
E
D000465:Algorithms; D000595:Amino Acid Sequence; D016208:Databases, Factual; D008969:Molecular Sequence Data; D017711:Nonlinear Dynamics