FEATnotator

FEATnotator annotates genomic features and analyzes sequence variations from NGS to calculate structural and translational effects and to contextualize positional information relative to genes and predicted protein binding sites.

Key Features:

• Integration of Genomic Datasets: Integrates user-defined genomic datasets, including next-generation sequencing (NGS) data, to associate experimental positions with annotated reference features such as genes and predicted protein binding sites.
• Handling Polymorphic Inputs: Calculates structural and translational effects of sequence variations on genes and proteins to evaluate impacts of polymorphic genomic inputs.
• Reporting Overlaps and Proximities: Reports overlaps and proximities between experimental positions and annotated features to contextualize positional information.
• Comprehensive Variation Summaries: Generates detailed summaries of genomic variations in relation to gene models and genic regions, including quantitative trait loci (QTL).
• Support for Non-model and Expanded References: Operates with non-model organisms and expanded model references to integrate diverse genomic annotations.

Scientific Applications:

• Variant interpretation in polymorphic samples: Evaluates effects of sequence variation on gene structure and protein translation for experiments with polymorphic inputs.
• Contextualizing NGS positional data: Associates NGS-derived positional information with annotated features to aid interpretation of genomic experiments.
• Whole-genome variation summarization: Summarizes whole-genome sequence variation in species such as Arabidopsis thaliana, including replication of discoveries like protein-coding deletions affecting root development.
• Analysis of single genes and QTL regions: Produces targeted summaries for investigation of single genes or genic regions such as QTL.

Methodology:

Integrates and analyzes user-defined datasets, associates NGS data with annotated reference features, calculates structural and translational effects of sequence variations on genes and proteins, reports overlaps and proximities, and generates summaries of genomic variation relative to gene models.