SAAVpedia

SAAVpedia identifies, annotates, and retrieves single amino acid variants (SAAVs) from proteomic and genomic datasets to confirm nonsynonymous single nucleotide variants (nsSNVs) at the protein level and prioritize pathogenic SAAV candidates.

Key Features:

• SAAVidentifier: Utilizes a comprehensive reference database containing over 18 million SAAVs and performs identification and quality assessment of SAAVs from proteomic data to detect amino acid sequence variants.
• SAAVannotator: Provides detailed functional annotations incorporating biological, clinical, and pharmacological information and enables condition-specific interpretation of SAAVs.
• SNV/SAAVretriever: Enables bidirectional mapping between nsSNVs and SAAVs across genomic and proteomic datasets and supports integrated retrieval of relevant variant data.
• SAAVvisualizer: Generates statistical plots based on the functional annotations of detected SAAVs for downstream analysis.

Scientific Applications:

• Proteogenomic Interpretation: Prioritizes and interprets SAAVs to identify true pathogenic variant candidates in proteogenomic studies.
• Disease Research: Applied to breast cancer and glioblastoma studies to identify genes with significant SAAVs, including BRCA2 and FAM49B.
• Human Proteome Project (HPP): Facilitates discovery of SAAVs to support protein functional studies within the HPP.

Methodology:

Use of a reference database of over 18 million SAAVs; identification and quality assessment of SAAVs from proteomic data; annotation with biological, clinical, and pharmacological information; bidirectional mapping between nsSNVs and SAAVs across datasets; generation of statistical plots based on functional annotations.