Premium
A novel graphical representation of protein sequences and its application
Author(s) -
Liao Bo,
Liao Benyou,
Lu Xinguo,
Cao Zhi
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21833
Subject(s) - representation (politics) , sequence (biology) , similarity (geometry) , protein sequencing , amino acid , domain (mathematical analysis) , class (philosophy) , computer science , basis (linear algebra) , algorithm , fourier transform , computational biology , peptide sequence , biological system , theoretical computer science , mathematics , artificial intelligence , chemistry , biology , biochemistry , mathematical analysis , geometry , politics , political science , law , image (mathematics) , gene
On the basis of information on the evolution of the 20 amino acids and their physiochemical characteristics, we propose a new two‐dimensional (2D) graphical representation of protein sequences in this article. By this representation method, we use 2D data to represent three‐dimensional information constructed by the amino acids' evolution index, the class information of amino acid based on physiochemical characteristics, and the order of the amino acids appearing in the protein sequences. Then, using discrete Fourier transform, the sequence signals with different lengths can be transformed to the frequency domain, in which the sequences are with the same length. A new method is used to analyze the protein sequence similarity and to predict the protein structural class. The experiments indicate that our method is effective and useful. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011