Pei Jimin, Grishin Nick V
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Methods Mol Biol. 2014;1079:263-71. doi: 10.1007/978-1-62703-646-7_17.
Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.
多序列比对（MSA）是生物信息学和计算生物学中一种具有多种应用的重要工具。为差异较大的蛋白质构建准确的多序列比对仍然是一项艰巨的计算任务。公共数据库中不断增加的蛋白质序列和结构可用于提高比对质量。PROMALS3D是一种用于构建蛋白质多序列比对的工具，它通过数据库搜索获得的额外进化和结构信息得到增强。PROMALS3D会自动从序列和结构数据库中识别输入蛋白质的同源物，从三维结构比对中推导基于结构的约束，并在基于一致性的框架中将它们与基于序列的profile-profile比对约束相结合，以构建高质量的多序列比对。PROMALS3D的输出是一个包含有关输入蛋白质及其同源物的序列和结构信息的一致性比对。PROMALS3D网络服务器和软件包可在http://prodata.swmed.edu/PROMALS3D获取。
