Pseudo amino acid composition (PseAAC) is an algorithm that could convert a protein sequence into a digital vector that could be processed by pattern recognition algorithms. The design of PseAAC incorporated the sequence order information to improve the conventional amino acid compositions. The application of pseudo amino acid composition is very common, including almost every branch of computational proteomics.



This is a major update to the PseAAC-Builder. We name it the "General" for its ability of generating many different modes of general form PseAAC. It is also called the PseAAC-Builder 3.0 in all source code and all technical documents

Linux/Unix Linux/UNIX platform

Windows+Cygwin Windows + Cygwin platform

Linux/Unix SourceForge Website

Binary Extension Module UpdatesUpdates

These are the Binary Extension Modules for supporting the Gene Ontology mode and the Functional Domain mode of PseAAC-General. We have deployed a server using Amazon EC2 to update the following modules automatically on the first day of every month.

GO mode BEM Latest update of the gene ontology mode

Functional Domain mode BEM Latest update of the functional domain mode

PseAAC-Builder Version 2.0

Linux/Unix SourceForge Website

PseAAC-Builder Version 1.05

SourceForge SourceForge Website


ManualA User Manual For PseAAC-Builder version 3.0

ManualA User Manual For BEM Online Update Tools

Related resources

CygwinCygwin Environment

Tcl/Tk Tcl / Tk


[1] Pufeng Du, Xin Wang, Chao Xu, Yang Gao. PseAAC-Builder: A cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. Analytical Biochemistry 425 (2012) pp.117-119

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[2] Pufeng Du, Shuwang Gu, Yasen Jiao. PseAAC-General: Fast building various modes of general form of Chou's pseudo-amino acid composition for large-scale protein datasets. International Journal of Molecular Sciences 15 (2014) pp.3495-3506

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Full TextFull text in MDPI


If you have any queries, questions or bug reports, please feel free to contact Dr. Pufeng Du. Email:

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