GTF/GFF3 Sequence Extractor

This tool retrieves nucleotide sequences from a genome assembly by applying a GTF/GFF3 annotation. It supports extracting exons, CDS, genes, or transcript regions, with optional strand-aware orientation and translation. Researchers supply a genome FASTA and an annotation file; the tool validates coordinates, resolves feature boundaries, and outputs a FASTA file with one sequence per requested feature. It is designed for reproducible workflows and can integrate into pipelines that require feature-specific sequences for primer design, alignment, or comparative analyses.
Conceptually, the tool parses the annotation, maps features to genomic coordinates, orders components (e.g., exons within a transcript), and concatenates sequences according to the feature type. On the negative strand, sequences are reverse-complemented when requested. Optional extensions allow upstream/downstream sequence context and translation of CDS to protein using the standard genetic code. Outputs can include metadata reports in CSV or BED formats to support downstream processing.
The primary beneficiaries are genomics researchers, bioinformaticians, and core facilities who need reliable, repeatable sequence retrieval for discovery, validation, or pipeline automation. By separating feature resolution, sequence extraction, and optional translation, the tool provides a clear, auditable trace of how each sequence was derived and how downstream analyses were generated.