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Methods Mol Biol. 2014;1079:263-71. doi: 10.1007/978-1-62703-646-7_17.

PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

Author information

1
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Abstract

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.

PMID:
24170408
PMCID:
PMC4506754
DOI:
10.1007/978-1-62703-646-7_17
[Indexed for MEDLINE]
Free PMC Article

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