Parallelization of the MAFFT multiple sequence alignment program.
Parallelization of the MAFFT multiple sequence alignment program.
复制标题
DOI：
10.1093/bioinformatics/btq224
复制
发表时间：
2010-08-01
期刊：
影响因子：
--
通讯作者：
Toh H
中科院分区：
文献类型：
--
作者：
Katoh K;Toh H
多序列比对（MSA）是比较序列分析中的重要步骤。网格化是减少大规模层序分析所需时间的关键技术。MAFFT MSA程序的三个计算阶段，全对全比较，渐进对齐和迭代细化，使用POSIX线程库并行化。两个自然的并行化策略（最佳优先和简单的爬山）的迭代细化阶段实施。基于两种方法的客观分数和基准分数的比较，我们选择了一个简单的爬山方法作为默认值。可用性：MAFFT的并行化版本可在http://mafft.cbrc.jp/alignment/software/上获得。此版本目前仅支持Linux操作系统。联系方式：kazutaka. aist.go.jp补充信息：补充数据可在生物信息学在线获得。
Summary: Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses. The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT MSA program were parallelized using the POSIX Threads library. Two natural parallelization strategies (best-first and simple hill-climbing) were implemented for the iterative refinement stage. Based on comparisons of the objective scores and benchmark scores between the two approaches, we selected a simple hill-climbing approach as the default. Availability: The parallelized version of MAFFT is available at http://mafft.cbrc.jp/alignment/software/. This version currently supports the Linux operating system only. Contact: kazutaka.katoh@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online.