Gene Cluster Product Similarity Search
1.0

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Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Gene Cluster Product Similarity Search , available in the GTN

Thanks to...

Tutorial Author(s): Paul Zierep

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1145?version=1

Inputs

ID Name Description Type
Jupyter Notebook Genbank2Features Jupyter Notebook Genbank2Features n/a
  • File
Query Genomes Query Genomes n/a
  • string?
Target Molecules (Natural Compound Library) Target Molecules (Natural Compound Library) n/a
  • File

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
  • File
NCBI Accession Download on input dataset(s): Downloaded Files NCBI Accession Download on input dataset(s): Downloaded Files n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
Antismash on input dataset(s): HTML report Antismash on input dataset(s): HTML report n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:03 by Helena Rasche

Added/updated 4 files


Open master 9b8b9c8
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
NCBI Resources
chemfp
antiSMASH
License
Creative Commons Attribution 4.0 International
Activity

Views: 352   Downloads: 83

Created: 25th Jun 2024 at 11:03

Last updated: 25th Jun 2024 at 11:03

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Total size: 131 KB
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