Pei Jimin, Tang Ming, Grishin Nick V
Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W30-4. doi: 10.1093/nar/gkn322. Epub 2008 May 24.
Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/.
多序列比对在计算序列和结构分析中至关重要，应用于同源性检测、结构建模、功能预测和系统发育分析。我们报告了PROMALS3D网络服务器，用于利用可用的3D结构、数据库同源物和预测的二级结构信息构建多个蛋白质序列和/或结构的比对。PROMALS3D比对精度高于其他一些先进方法。PROMALS3D网络服务器的输入可以是FASTA格式的蛋白质序列、PDB格式的蛋白质结构和/或用户定义的比对约束。输出页面提供多种格式的比对结果，包括带有关于序列分组、预测二级结构和共有序列有用信息的彩色比对。还可获取序列和结构数据库搜索的中间结果。PROMALS3D网络服务器网址为：http://prodata.swmed.edu/promals3d/ 。
