ParaAT (Parallel Alignment and back-Translation) is capable of manipulating a large number of homologous groups. ParaAT features parallel construction of multiple protein-coding DNA alignments and thus is well suited for large-scale data analysis in the high-throughput era.

  • Back-translated nucleotide alignments guided by amino acid alignments are more reliable and accurate than direct nucleotide alignments.
  • Extant tools developed for automating back-translated nucleotide alignments accept only one homologous group as input and thus are incapable of processing a large number of homologs.
  • Constructing multiple homologous alignments for protein-coding DNA sequences is crucial for a variety of bioinformatic analyses but remains computationally challenging.
  • With the growing amount of sequence data and the ongoing efforts largely dependent on protein-coding DNA alignments, there is an increasing demand for a tool capable of processing a large number of homologous groups.

ParaAT involves two parallel regions, in which the master thread creates a team of slave threads running concurrently. In the first parallel region, ParaAT aligns protein sequences for multiple homologs by assigning each homolog to one of the slave threads. In the second region, ParaAT parallelly back-translates protein sequence alignments into the corresponding DNA alignments.

ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks.


  1. Zhang, Z., Xiao, J., Wu, J., Zhang, H., Liu, G., Wang, X. and Dai, L. (2012) ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments, Biochem Biophys Res Commun, 419(4):779-7

Basic Infomation

ContributorsZhang Z., Xiao J., Wu J., Zhang H., Liu G., Wang X., Dai L
Created AtSeptember 28, 2016
Updated AtOctober 31, 2016

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Homolog group file

File containing multiple amino acid sequences

File containing multiple nucleotide sequences

Output file format