title: SMA: An Efficient Tool for Large-Scale Multiple Alignment.
abstract: 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.
authors.affiliation: School of Mathematics and LPMC, Nankai University, Tianjin 300071, China. Email: d021867@mail.nankai.edu.cn.
authors.forename: Shiyi
authors.initials: S
authors.lastname: Shen
authors.forename: Liuhuan
authors.initials: L
authors.lastname: Dong
authors.forename: Kui
authors.initials: K
authors.lastname: Wang
authors.forename: Gang
authors.initials: G
authors.lastname: Hu