Gene Cluster Product Similarity Search 1.0
Visit source
Download RO-Crate
Run on GalaxyAssociated Tutorial
This workflows is part of the tutorial Secondary metabolite discovery, available in the GTN
Thanks to...
Tutorial Author(s): Paul Zierep
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Jupyter Notebook Genbank2Features | Jupyter Notebook Genbank2Features | n/a |
|
| Query Genomes | Query Genomes | n/a |
|
| Target Molecules (Natural Compound Library) | Target Molecules (Natural Compound Library) | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | NCBI Accession Download | toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 |
| 4 | Molecule to fingerprint | toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5 |
| 5 | Antismash | toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1 |
| 6 | Collapse clusters in one Genbank entry | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 7 | Extract SMILES qualifiers | interactive_tool_jupyter_notebook |
| 8 | Convert table to smi format | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 9 | Remove beginning | Remove beginning1 |
| 10 | Remove duplicated molecules | toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates/3.1.1+galaxy0 |
| 11 | Molecule to fingerprint | toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5 |
| 12 | Natural Product | toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1 |
| 13 | Drug-likeness | toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0 |
| 14 | Similarity Search | toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| NCBI Accession Download on input dataset(s): Log | NCBI Accession Download on input dataset(s): Log | n/a |
|
| NCBI Accession Download on input dataset(s): Downloaded Files | NCBI Accession Download on input dataset(s): Downloaded Files | n/a |
|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
|
| Antismash on input dataset(s): HTML report | Antismash on input dataset(s): HTML report | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
Version History
master
Creators and Submitter
Views: 1125 Downloads: 161 Runs: 0
Created: 2nd Jun 2025 at 10:58
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
