strictlyincludegff
strictlyincludegff filters GFF (General Feature Format) entries to identify and print genomic elements that are strictly contained within a specified template for genome annotation and comparative genomics.
Key Features:
- Element Identification: Filters and outputs genomic features from GFF files that are completely contained within a provided template region.
- GFF File Support: Operates on GFF (General Feature Format) input to select strictly included features for downstream analysis.
- Galaxy Integration: Executes within the Galaxy framework and interfaces with Galaxy workflows and services.
Scientific Applications:
- Genome Annotation: Refines annotations by selecting features strictly nested within target regions to ensure precise feature assignment.
- Comparative Genomics: Enables comparison of conserved or unique nested features across species or strains by extracting strictly included elements.
Methodology:
Integrates with the Galaxy platform via the Galaxy API and uses the Bioblend library for execution; implemented as part of custom web services around the Galaxy@Pasteur instance.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
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.