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

doi:10.3390/ijms15033495

PseAAC-General: fast building various modes of general form of Chou's pseudo-amino acid composition for large-scale protein datasets

Int J Mol Sci. 2014 Feb 26;15(3):3495-506. doi: 10.3390/ijms15033495.

Authors

Pufeng Du¹, Shuwang Gu², Yasen Jiao³

Affiliations

¹ School of Computer Science and Technology, Tianjin University, Tianjin 300072, China. pufengdu@gmail.com.
² School of Computer Science and Technology, Tianjin University, Tianjin 300072, China. shuwanggu@gmail.com.
³ School of Computer Science and Technology, Tianjin University, Tianjin 300072, China. yasenjiao@gmail.com.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acids / chemistry*
Computational Biology / methods*
Databases, Protein*
Proteins / chemistry*
Reproducibility of Results
Software*

Substances

Amino Acids
Proteins