genbank2gff3
genbank2gff3 converts sequence annotations from GenBank, EMBL, and UniProt formats into GFF3 to standardize genomic feature representations for downstream computational analyses.
Key Features:
- Format conversion: Converts sequence annotation files from GenBank, EMBL, and UniProt into GFF3 (General Feature Format version 3).
- Galaxy integration: Compatible with the Galaxy platform and Galaxy@Pasteur for integration into Galaxy-based workflows.
- API invocation: Can be invoked through the Galaxy API or via the Bioblend library for programmatic execution.
- Cluster execution: Runs using the Galaxy@Pasteur execution engine on the Institut Pasteur cluster.
Scientific Applications:
- Genomic research: Provides standardized GFF3 annotations for comparative genomics, gene prediction, and functional annotation studies.
- Metagenomics and phylogenetics: Supplies GFF3-formatted annotations to support metagenomic data analysis and phylogenetic investigations.
- Workflow integration: Enables incorporation of converted annotations into Galaxy-based bioinformatics pipelines for reproducible computational analyses.
Methodology:
Operates within the Galaxy framework and can be invoked via the Galaxy API or the Bioblend library, running on the Galaxy@Pasteur execution engine on the Institut Pasteur cluster.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
Data Inputs & Outputs
Data retrieval
Publications
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. 2016;44(W1):W3-W10. doi:10.1093/nar/gkw343. PMID:27137889. PMCID:PMC4987906.
Mareuil F, Doppelt-Azeroual O, Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services. Unknown Journal. 2017. doi:10.7490/f1000research.1114334.1.