VarMap

VarMap maps genomic variants specified by chromosome coordinates onto canonical UniProt protein residues and associates them with protein 3D structures to enable interpretation of variant effects in the context of alternative splicing and transcript variation.

Key Features:

• Mapping Functionality: Translates chromosome coordinates into specific residues in canonical UniProt protein sequences.
• 3D Structural Contextualization: Associates mapped residues with relevant protein 3D structures to provide spatial context.
• Validation Checks: Performs checks to confirm correct association of genomic coordinates with their respective protein sequences and structural annotations.
• Structural Annotation: Annotates mapped variants with structural information relevant to protein stability, interactions, and function.

Scientific Applications:

• Variant Interpretation: Distinguishes between benign and pathogenic genetic variants by providing structural context of mapped residues.
• Molecular Consequence Analysis: Supports studies of how genomic alterations affect protein conformation and function in genetics and molecular biology.
• Clinical and Translational Research: Facilitates variant impact prediction, disease modeling, and identification of potential therapeutic targets in personalized medicine.

Methodology:

Maps chromosome coordinates to residues in canonical UniProt sequences while accounting for alternative splicing and transcript evidence, integrates mappings with protein 3D structures, and applies validation checks for sequence and structural annotations.