首页> 外文期刊>Nucleic acids research >SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
【24h】

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction

机译:SATCHMO-JS:用于同时进行蛋白质多序列比对和系统进化树构建的网络服务器

获取原文
           

摘要

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM–HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.
机译:我们提出了使用隐马尔可夫模型(SATCHMO-JS)网络服务器的快速启动同时比对和树结构,用于同时估计蛋白质多序列比对(MSA)和系统树。服务器将FASTA格式的一组序列作为输入,并输出系统树和MSA。这些可以在线查看或从网站下载。 SATCHMO-JS是SATCHMO算法的扩展,并采用分而治之的策略在系统发生树的更高位置上启动SATCHMO,从而降低了逐步进行的HMM-HMM评分的计算复杂性和对齐。来自PREFAB基准数据集的983个结构对齐对的基准数据集的结果表明,相比于MUSCLE,使用快速傅里叶变换(MAFFT)的多重对齐,ClustalW和原始的SATCHMO算法,SATCHMO-JS在统计精度上提供了统计学上显着的提高。 SATCHMO-JS Web服务器可从http://phylogenomics.berkeley.edu/satchmo-js获得。这些实验中使用的数据集可从http://phylogenomics.berkeley.edu/satchmo-js/supplementary/下载。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱:kefu@zhangqiaokeyan.com

京公网安备:11010802029741号 ICP备案号:京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有
  • 客服微信

  • 服务号