NRAlign (Neighboring Residue Alignment) is a multiple sequence alignment program that makes better use of horizontal information by taking into account alignment of neighboring residues when aligning two residues. We test NRAlign on benchmark multiple protein sequence alignments, including BAliBASE 3.0, HOMSTRAD, PREFAB 4.0, and SABmark 1.65, and benchmark multiple DNA/RNA sequence alignments, including BRAliBase II, and DNA PREFAB, by modifying existing multiple alignment algorithms TCoffee, MUSCLE, ProbCons, and MUMMALS (only for protein sequence alignment) to make use of horizontal information. We show that consistent average improvements can be obtained and the improvements in accuracy can be as much as a few percent on protein sequence alignment and as much as 5 to 10% on DNA/RNA sequence alignment.
NRAlign is available for download as modified versions of TCoffee 5.31, MUSCLE 3.6, ProbCons 1.10, and MUMMALS 1.01. The following steps will create a directory called nralign. Further instructions are in the README file.
Lu Y. and Sze S.-H. (2009) Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Research, 37, 463-472.