SMA: An Efficient Tool for Large-Scale Multiple Alignment

To compare large numbers of genomic sequences of related virus, such as HIV, biologists have an increasing need for a method that can efficiently handle hundreds, even thousands, of genomic sequences accurately enough to correctly align these conserved features. In this paper, we introduce a new and efficient tool named SMA that can easily accommodate large-scale virus genomic sequences. A high-throughput test on 706 HIV-1 genomic sequences shows that SMA is much faster than the available programs with at least the same performance. SMA is a good improvement of existing algorithms for high-volume multiple sequence alignment. It offers an option that provides improved speed and accuracy compared with currently available programs. SMA is freely available at http://mathbio.nankai.edu.cn/e_version/align_query.php