TransAT

TransAT annotates genetic variants at the transcript level by converting RefSeq IDs to Ensembl IDs, mapping genomic positions, and retrieving SNP identifiers, allele frequencies across global populations, and gene annotations for variant interpretation.

Key Features:

• Transcript-level input: Accepts transcript identifiers to perform annotations directly at the transcript level and return corresponding variant information.
• RefSeq-to-Ensembl conversion: Converts RefSeq IDs to Ensembl IDs to enable cross-referenced transcript annotation.
• SNP identification and genomic mapping: Maps transcript information to genomic positions and returns corresponding SNP IDs and genomic coordinates.
• Allele frequency retrieval: Obtains allele frequencies for SNPs across various global populations from publicly available genomic data.
• Gene annotation retrieval: Retrieves gene-level annotations associated with queried transcripts and variants.
• Comparative frequency analysis: Performs comparative analyses of SNP frequencies between diseased and general populations using public genomic datasets.
• Pathogenicity-relevant annotation: Identifies variants occurring in coding regions or regulatory sequences that may influence protein function and gene expression.

Scientific Applications:

• Precision medicine / Pharmacogenomics: Correlates transcript-level variants and allele frequencies with therapeutic response and individualized treatment considerations.
• Variant interpretation and pathogenicity assessment: Supports assessment of variant impact on protein function and gene expression, particularly for coding and regulatory variants.
• Population genetics: Enables analysis of allele frequency distributions across global populations for population-specific variant prevalence studies.
• Transcriptional and translational profiling studies: Integrates transcript-level variant annotations with gene annotations to support studies of transcriptional and translational effects.

Methodology:

Converts RefSeq IDs to Ensembl IDs, maps transcript information to genomic positions to obtain SNP IDs and coordinates, retrieves allele frequencies and gene annotations from publicly available genomic databases, and performs comparative SNP frequency analyses between diseased and general populations to identify variants that may affect protein function or gene expression.