PseAAC-General: Fast Building Various Modes of General Form of Chou's Pseudo-Amino Acid Composition for Large-Scale Protein Datasets

Pufeng Du*, Shuwang Gu, Yasen Jiao

*Corresponding author for this work

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

255 Citations (Scopus)
50 Downloads (CityUHK Scholars)

Abstract

The general form pseudo-amino acid composition (PseAAC) has been widely used to represent protein sequences in predicting protein structural and functional attributes. We developed the program PseAAC-General to generate various different modes of Chou's general PseAAC, such as the gene ontology mode, the functional domain mode, and the sequential evolution mode. This program allows the users to define their own desired modes. In every mode, 544 physicochemical properties of the amino acids are available for choosing. The computing efficiency is at least 100 times that of existing programs, which makes it able to facilitate the extensive studies on proteins and peptides. The PseAAC-General is freely available via SourceForge. It runs on both Linux and Windows.
Original languageEnglish
Pages (from-to)3495-3506
Number of pages12
JournalInternational Journal of Molecular Sciences
Volume15
Issue number3
Online published26 Feb 2014
DOIs
Publication statusPublished - Mar 2014

Funding

This work was supported by National Science Foundation of China (NSFC 61005041); Specialized Research Fund for the Doctoral Program of Higher Education (SRFDP 20100032120039); Tianjin Natural Science Foundation (No. 12JCQNJC02300); China Post-doctoral Science Foundation (2012T50240 and 2013M530114); HK Scholar Program (XJ2012033) and the Seed Foundation of Tianjin University (No. 60302006 and 60302024).

Research Keywords

  • general form
  • large-scale datasets
  • pseudo-amino acid composition
  • DISCRETE WAVELET TRANSFORM
  • SUPPORT VECTOR MACHINE
  • PREDICTING SUBCELLULAR-LOCALIZATION
  • ENZYME SUBFAMILY CLASSES
  • COUPLED RECEPTOR CLASSES
  • OUTER-MEMBRANE PROTEINS
  • STRUCTURAL CLASS
  • MULTIPLE SITES
  • APPROXIMATE ENTROPY
  • WEB-SERVER

Publisher's Copyright Statement

  • This full text is made available under CC-BY 3.0. https://creativecommons.org/licenses/by/3.0/

Fingerprint

Dive into the research topics of 'PseAAC-General: Fast Building Various Modes of General Form of Chou's Pseudo-Amino Acid Composition for Large-Scale Protein Datasets'. Together they form a unique fingerprint.

Cite this