Issue 10, 2015

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

Abstract

With the avalanche of DNA/RNA sequences generated in the post-genomic age, it is urgent to develop automated methods for analyzing the relationship between the sequences and their functions. Towards this goal, a series of sequence-based methods have been proposed and applied to analyze various character-unknown DNA/RNA sequences in order for in-depth understanding their action mechanisms and processes. Compared with the classical sequence-based methods, the pseudo nucleotide composition or PseKNC approach developed very recently has the following advantages: (1) it can convert length-different DNA/RNA sequences into dimension-fixed digital vectors that can be directly handled by all the existing machine-learning algorithms or operation engines; (2) it can contain the desired features and properties according to the selection or definition of users; (3) it can cover considerable sequence pattern information, both local and global. This minireview is focused on the concept of pseudo nucleotide composition, its development and applications.

Graphical abstract: Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

Article information

Article type
Review Article
Submitted
27 févr. 2015
Accepted
05 juin 2015
First published
05 juin 2015

Mol. BioSyst., 2015,11, 2620-2634

Author version available

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

W. Chen, H. Lin and K. Chou, Mol. BioSyst., 2015, 11, 2620 DOI: 10.1039/C5MB00155B

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