airpg

airpg assesses and validates inverted repeat annotations in plastid genomes to improve annotation reliability for downstream analyses.

Key Features:

• Automated retrieval from NCBI Nucleotide: Automatically accesses plastid genome sequences from the NCBI Nucleotide database with configurable search parameters.
• Configurable search parameters: Allows specification of variable search parameters to control the scope of genome retrieval.
• Inverted repeat annotation surveying: Surveys each retrieved genome for annotations related to inverted repeat length and location.
• Sequence self-comparison for IR confirmation: Performs self-comparisons of genome sequences to confirm or refute annotated inverted repeat regions.
• Duplicate record management: Identifies and removes duplicate genome records to ensure unique dataset entries.
• Handling taxa lacking inverted repeats: Accounts for taxa that genuinely lack inverted repeats when assessing annotation presence or absence.
• Statistical analysis of metadata: Examines associations between genome record metadata (such as release year and publication status) and inverted repeat annotation completeness or accuracy.

Scientific Applications:

• Quality control of plastid genomes: Identifies incomplete or incorrect inverted repeat annotations to improve dataset quality for comparative and evolutionary studies.
• Data reliability assessment: Validates annotation accuracy so downstream analyses rely on correctly annotated plastid genomic data.
• Annotation trend analysis: Correlates annotation accuracy with metadata to investigate temporal or publication-related trends in submission quality.

Methodology:

Automated retrieval of plastid genomes from NCBI Nucleotide using configurable search parameters; surveying genome annotations for inverted repeat length and location; performing self-comparisons of genome sequences to confirm inverted repeats; identifying and removing duplicate genome records; and conducting statistical analyses relating record metadata (release year, publication status) to inverted repeat annotation completeness and accuracy.