Protein sequence analysis by incorporating modified chaos game and physicochemical properties into Chou's general pseudo amino acid composition

J Theor Biol. 2016 Oct 7:406:105-15. doi: 10.1016/j.jtbi.2016.06.034. Epub 2016 Jun 29.

Abstract

In this contribution we introduced a novel graphical method to compare protein sequences. By mapping a protein sequence into 3D space based on codons and physicochemical properties of 20 amino acids, we are able to get a unique P-vector from the 3D curve. This approach is consistent with wobble theory of amino acids. We compute the distance between sequences by their P-vectors to measure similarities/dissimilarities among protein sequences. Finally, we use our method to analyze four datasets and get better results compared with previous approaches.

Keywords: Codon; Hydropathy index; Isoelectric point; Protein vector; Sequences analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Animals
  • Chemical Phenomena*
  • Codon / genetics
  • Game Theory*
  • Humans
  • Nonlinear Dynamics*
  • Phylogeny
  • Sequence Analysis, Protein / methods*
  • Transcription Factors / metabolism
  • beta-Globins

Substances

  • Amino Acids
  • Codon
  • Transcription Factors
  • beta-Globins