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.
Keywords
Protein structure databaseSequence (biology)Sequence alignmentConstruct (python library)Computer scienceMultiple sequence alignmentAlignment-free sequence analysisConsistency (knowledge bases)Structural alignmentComputational biologyProtein superfamilyTask (project management)Protein sequencingData miningInformation retrievalSequence databaseBiologyPeptide sequenceArtificial intelligenceGeneticsEngineeringProgramming languageGene
MeSH Terms
Computational BiologyEvolutionMolecularInternetProtein ConformationProteinsSequence AlignmentSoftware
Affiliated Institutions
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Publication Info
- Year
- 2013
- Type
- article
- Volume
- 1079
- Pages
- 263-271
- Citations
- 242
- Access
- Closed
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Cite This
Jimin Pei,
Nick V. Grishin
(2013).
PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information.
Methods in molecular biology
, 1079
, 263-271.
https://doi.org/10.1007/978-1-62703-646-7_17
Identifiers
- DOI
- 10.1007/978-1-62703-646-7_17
- PMID
- 24170408
- PMCID
- PMC4506754