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Representation of amino acid sequences as two‐dimensional point patterns
Author(s) -
Pleißner KlausPeter,
Wernisch Lorenz,
Oswald Helmut,
Fleck Eckart
Publication year - 1997
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.1150181504
Subject(s) - amino acid , representation (politics) , sequence (biology) , protein sequencing , peptide sequence , plot (graphics) , protein methods , amino acid residue , sequence logo , computational biology , sequence analysis , biology , dna , sequence alignment , mathematics , genetics , gene , statistics , politics , political science , law
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.