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Update links and funders
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Marie59 authored Oct 3, 2024
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key_points:
- "RO-Crate in earth-system analysis"
- "Marine omics workflow "
contributors:
- Marie59

contributions:
authorship:
- Marie59
funding:
- fairease
- eurosciencegateway
---

# Workflow context

The workflow used as an example here goes from :
- First, produce a protein FASTA file from a nucleotide FASTA file using Prodigal (a tool that predicts protein-coding genes from DNA sequences).
- Then, use InterProscan to create a tabular. Interproscan is a batch tool to query the InterPro database. It helps identify and predict the functions of proteins by comparing them to known databases.
- Finally, discover SanntiS both to build genbank and especially to detect and annotate biosynthetic gene clusters (BGCs).
- First, produce a protein FASTA file from a nucleotide FASTA file using [Prodigal](tool_id=toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0) (a tool that predicts protein-coding genes from DNA sequences).
- Then, use [InterProscan](toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3) to create a tabular. Interproscan is a batch tool to query the InterPro database. It helps identify and predict the functions of proteins by comparing them to known databases.
- Finally, discover [SanntiS](toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1) both to build genbank and especially to detect and annotate biosynthetic gene clusters (BGCs).
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## The workflow itself
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## Run the workflow

Import and run the following workflow https://earth-system.usegalaxy.eu/u/marie.josse/w/marine-omics-identifying-biosynthetic-gene-clusters
Import and run the [Biosynthetic Gene Clusters workflow]({% https://earth-system.usegalaxy.eu/u/marie.josse/w/marine-omics-identifying-biosynthetic-gene-clusters %})

To know more on how to do that follow the tutorial https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/tutorial.html
To know more on how to do that follow the [tutorial]({% https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/tutorial.html %})
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## Generate the RO-Crate

Once you run the workflow you can generate the RO-Crate. To do so follow the tutorial https://training.galaxyproject.org/training-material/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html
Once you run the workflow you can generate the RO-Crate. To do so follow the [tutorial]({% https://training.galaxyproject.org/training-material/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html %})
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