TreeDomViewer

TreeDomViewer visualizes phylogenetic relationships alongside protein domain architectures to support genome annotation and evolutionary analysis.

Key Features:

• Phylogenetic Tree Construction: Generates phylogenetic trees from input sequences to represent evolutionary relationships among proteins or gene products.
• Multiple Sequence Alignment Integration: Projects protein domain annotations onto multiple sequence alignments to display conserved and divergent regions across homologs.
• InterProScan Data Utilization: Incorporates InterProScan domain predictions to annotate protein sequences with domain, family, and functional signatures.
• Domain-architecture-based Homology Detection: Enables detection and comparison of homologous sequences based on shared domain architectures even when amino acid or nucleotide identity is not statistically significant.
• Scalable Vector Graphics Output: Produces scalable vector graphics summarizing orthology and domain content for visual comparison and publication-quality figures.

Scientific Applications:

• Protein Evolution Analysis: Combine phylogenetic trees and domain architectures to study the evolution of proteins and protein complexes.
• Functional Inference of Unknown Proteins: Infer functions of unknown or poorly characterized homologs through comparative domain analysis.
• Genome and Gene Annotation Support: Support annotation pipelines for novel genes or gene products by aligning and comparing domain structures across sequences.
• Analysis of Divergent Families: Provide functional insights among highly divergent family members by comparing domain architectures rather than relying solely on sequence identity.

Methodology:

Performs multiple sequence alignment, constructs phylogenetic trees, incorporates InterProScan domain predictions, and projects domain annotations onto alignments to compare domain structures and infer functions based on domain architecture and amino acid substitutions.