Plastid

Plastid provides nucleotide-resolution representations and analysis of genomics and next-generation sequencing (NGS) read alignments.

Key Features:

• Nucleotide-Resolution Analysis: Performs nucleotide-by-nucleotide analyses of NGS data and read alignments.
• Generalized Framework: Implements a generalized framework adaptable to diverse NGS assays and experimental setups.
• Data Representation: Represents genomic and transcriptomic data as arrays of values associated with specific genomic positions, capturing alignment coordinates and fragment lengths relevant to assays such as ribosome profiling.
• Conversion and Manipulation Tools: Converts data from diverse sources into a standardized array format and manipulates discontinuous genomic features such as spliced transcripts with nucleotide precision.
• Coordinate Conversion: Automatically converts between genomic and feature-centric coordinates, accounting for splicing and strand orientation.
• Intuitive Data Models: Employs consistent biological idioms in its data models to represent genomic features and annotations.

Scientific Applications:

• RNA-seq: Used to analyze RNA sequencing (RNA-seq) data at nucleotide resolution.
• Ribosome profiling: Applied to ribosome profiling where read alignment coordinates and fragment lengths are informative.
• DMS-seq: Applied to dimethyl sulfate sequencing (DMS-seq) data.
• ORF-RATER integration: Integrated into ORF-RATER for open reading frame annotation.
• Novel NGS assays: Supports development and analysis of novel NGS assays via generalizable data representations.

Methodology:

Extracts assay-specific information from read alignments, represents biological data as arrays linked to genomic positions, converts inputs from diverse sources into standardized arrays, manipulates discontinuous (spliced) features, and performs automatic conversion between genomic and feature-centric coordinates accounting for splicing and strand orientation.