CAUSA: Codon and Amino-acid Unified Sequence Alignments

Structurally and Evolutionarily Consistent Alignment of Closely-related Proteins

Multiple sequence alignment (MSA) has been widely used for evolutionary analysis and structures modeling of proteins. Traditionally, proteins and their coding DNA sequences (CDSs) are aligned and analyzed separately, while often drastically different conclusions were drawn on a same set of data.

Here we present a new alignment strategy, codon and amino acid unified sequence alignment (CAUSA), which aligns protein sequences and their CDSs in a unified manner. Taken every codon as a whole but divisible unit, CAUSA allows internal gap placement, and enhanced the information content of MSAs.

CAUSA not only gives highly accurate alignment suitable for evolutionary analysis of closely-related proteins, but also explains how base/AA substitutions, insertions and deletions edit coding DNA sequences and drive protein structure evolution, through some unexplored ways of codons changes, including codon fusion, codon splitting and insertional partial frame shift.

Using the envelop protein (gp120) of the human immune deficiency virus (HIV) as a model, it is demonstrated that CAUSA is evolutionarily and structurally more accurate and consistent than traditional DNA, protein or codon level alignments.

In addition, CAUSA is computationally more efficient than codon level alignment methods.

Welcome to download the CAUSA software, latest version 2.1.18! It is free!

Download here.

We are still working on this software to make it better and provide data to prove it’s advantages.

Related publications:

  1. Wang Xiaolong, Yang Chao. (2015) CAUSA 2.0: accurate and consistent evolutionary analysis of proteins using codon and amino acid unified sequence alignments. PeerJ PrePrints 3:e1486
  2. Wang Xiaolong, Fu Yu , Zhao Yue , Wang Qi , Pedamallu Chandra Sekhar , Xu,Shuang-yong , Niu Yingbo , and Hu Jingjie. (2011) Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA). Available from Nature Precedings <>

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