GFF3GenBank

GFF3GenBank is a term used in genome annotation workflows to denote the integration of GFF3-style feature annotations with GenBank-style sequence records. While not a formal file format, it describes a common data representation and set of practices for moving annotation data between GFF3 and GenBank ecosystems.

GFF3 provides feature types, coordinates, strand information, and attributes in a tab-delimited file. GenBank records combine a flatfile sequence description with a FEATURES table that encodes evidence about genomic features using qualifiers. GFF3GenBank workflows aim to map GFF3 features to GenBank feature keys and qualifiers, maintain hierarchical relationships, and preserve cross-references to identifiers and metadata. The result is a GenBank-like annotated record suitable for submission or archiving, or an intermediate representation used in pipelines.

Implementation and tools for GFF3GenBank typically involve parsing both formats and performing ID mapping, coordinate normalization, and feature translation. Several bioinformatics libraries support reading and writing GenBank and GFF3 data, enabling programmatic conversion workflows. In practice, dedicated converters and pipelines may implement validation steps to ensure adherence to GenBank submission rules and data integrity.

Limitations include that not all GFF3 qualifiers have direct GenBank equivalents, and some complex relationships or nested features may require custom handling. Careful validation and, when necessary, manual curation are often needed to produce a compliant GenBank record.

Applications of GFF3GenBank concepts include facilitating data exchange between annotation tools, enabling GenBank submissions, and supporting interoperability within genomic data archives and research pipelines. See also GFF3, GenBank, GenBank format, and Biopython.