GAD

GAD extracts and manipulates genome feature annotations from GTF and GFF3 files to support downstream genomic analyses such as functional annotation, comparative genomics, and transcriptomic studies.

Key Features:

• Supported formats: Reads GTF and GFF3 annotation files and produces outputs in BED, GTF/GFF3, and FASTA formats.
• Feature extraction capabilities: Precisely extracts upstream genes, downstream genes, intergenic regions, genes, transcripts, exons, introns, coding sequences (CDS), 5' UTRs, 3' UTRs, and handles ambiguous sequence ontology terms.
• Batch processing: Supports analysis of multiple genome sequence and annotation files simultaneously to process large datasets.
• Implementation: Implemented in Python using coded functions for parsing and feature extraction from annotation files.
• Scalability: Designed to operate on large-scale genomic datasets for integration into analysis workflows.

Scientific Applications:

• Functional annotation: Extracted features can be used to assign functions to genomic elements and support downstream annotation tasks.
• Comparative genomics: Enables extraction of homologous feature sets and intergenic regions for cross-species comparison.
• Transcriptomic studies: Provides transcript, exon, intron, CDS, and UTR coordinates for RNA-seq mapping and expression analyses.
• Gene annotation pipelines: Supplies standardized feature outputs (BED, GTF/GFF3, FASTA) for integration into gene annotation workflows.

Methodology:

Parses GTF and GFF3 annotation files with Python-coded functions to interpret annotation records and extract specified genomic features, then writes outputs in BED, GTF/GFF3, or FASTA formats.