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Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81. doi: 10.1016/j.bbrc.2012.02.101. Epub 2012 Feb 27.

ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments.

Author information

1
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China. zhangzhang@big.ac.cn

Abstract

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 available and the ongoing efforts largely dependent on protein-coding DNA alignments, there is an increasing demand for a tool that can process a large number of homologous groups and generate multiple protein-coding DNA alignments. Here we present a parallel tool - ParaAT that is capable of parallelly constructing multiple protein-coding DNA alignments for a large number of homologs. As testified on empirical datasets, 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. ParaAT is freely available for academic use only at http://cbb.big.ac.cn/software.

PMID:
22390928
DOI:
10.1016/j.bbrc.2012.02.101
[Indexed for MEDLINE]

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