NGS-SNP

NGS-SNP annotates single nucleotide polymorphisms (SNPs) from whole-genome sequencing using Ensembl reference sequences to provide functional and comparative annotations.

Key Features:

• Rich annotations: Provides a wide array of SNP annotations, including annotations not commonly available in other SNP annotation tools.
• Orthologous sequence comparisons: Compares orthologous sequences to identify SNPs that affect conserved residues or modify residues/genes associated with phenotypes in other species.
• Ensembl compatibility: Leverages reference sequences from Ensembl and applies to any organism with Ensembl reference sequences.
• Script-based implementation: Implements annotation functionality as a collection of command-line scripts for automated SNP annotation workflows.

Scientific Applications:

• Functional impact inference: Identifies conserved residues affected by SNPs to infer potential impacts on protein function and evolutionary conservation.
• Cross-species phenotype mapping: Links SNPs to residues or genes associated with phenotypic traits across species to support comparative genomics studies.
• Genomic research and applied genomics: Supports analyses in basic research and applied genomics that require detailed SNP functional and comparative annotation.

Methodology:

Annotates SNPs using Ensembl reference sequences and performs orthologous sequence comparisons to assess conservation and associations with phenotypes.