Genomics & Bioinformatics Tools

Reference map of bioinformatics tools, databases, and resources used in STRC Gene research and Misha’s hearing loss investigation.

Variant Annotation & Interpretation

• dbNSFP — pre-computed functional predictions for all possible coding SNVs
• VariantValidator — HGVS nomenclature validation and transcript mapping
• DECIPHER — clinical interpretation of rare variants with phenotype data
• tmVar — text-mining tool for extracting variant mentions from literature
• variant tools (vtools) — command-line variant manipulation toolkit
• DDGun — DDGun3D — protein stability change prediction from mutations
• AlphaMissense — deep learning pathogenicity prediction for missense variants
• AbSplice2 — splicing effect prediction using tissue-specific features

Population Databases

• BRAVO — TOPMed — Trans-Omics for Precision Medicine variant frequencies
• ExAC (Legacy) — Exome Aggregation Consortium (precursor to gnomAD)
• CMDB (Chinese Millionome) — Chinese population variant frequencies
• Biobank Japan (BBJ) — PheWeb — Japanese population biobank phenotype-genotype browser
• KoB — KDNA — Korean Biodiversity / Korean DNA database

Protein Structure & Function

• SWISS-MODEL — automated protein homology modeling
• AlphaFold 3 Server — AI protein structure prediction
• AlphaFold Database — pre-computed structure predictions
• NetGPI — GPI-anchor prediction
• NetNGlyc — N-glycosylation site prediction
• Eigen — Eigen-PC — functional annotation scores combining multiple predictors

Literature & Data Mining

• PubTator — biomedical text-mining with named entity recognition
• LitVar 2.0 — literature search focused on genetic variants
• LitSense — AI-powered biomedical literature search
• LitSuggest — automated article recommendation for curators
• Europe PMC — European biomedical literature repository
• Semantic Scholar — AI-powered academic search engine

Genomic Infrastructure

• Galaxy Project — web-based platform for accessible bioinformatics workflows
• UCSC LiftOver — genome coordinate conversion between assemblies
• CrossMap — alternative tool for genome coordinate conversion
• Illumina Connected Insights — clinical genomics interpretation platform
• Mutalyzer — sequence variant nomenclature checker
• Terra.bio — cloud genomics analysis platform
• Evo — Evo 2 — long-context genomic foundation model (7B params, 131K context)
• ARCHS4 — RNA-seq expression data for all human genes
• AlphaGenome — DeepMind model for predicting variant effects on gene regulation

Gene Therapy Specific

• DB-OTO Trial Resources — database of inner ear gene therapy clinical trials
• ASGCT Gene Therapy Database — American Society of Gene & Cell Therapy trial registry
• AAV Capsid Database — adeno-associated virus capsid variants for gene delivery

Connections

• STRC Gene — primary research target
• DFNB16 Hearing Loss — the condition these tools help investigate
• MISHA Foundation — parent-driven research initiative
• [part-of] MOC - Psychology & ADHD — via Misha’s neurodevelopmental context