Research output per year
Research output per year
Description
Additional data for 'iPRESTO: automated discovery of biosynthetic sub-clusters linked to specific natural product substructures'.
Contents:
- antismashdb_dataset_tokenised_bgcs_clusterfile.csv contains the pre-processed BGCs (tokenised and filtered) from the antiSMASH-DB dataset. Genes are separated by commas and domains by semicolons.
- Pfam_100subs_tc.hmm is the unpressed Pfam database, additionally containing subPfam HMMs for the 112 most important biosynthetic Pfams.
- PRESTO-STAT_subclusters.txt contains all sub-clusters found by PRESTO-STAT applied to the antiSMASH-DB dataset.
- lda_model and files with lda_model* are the LDA model trained and used by PRESTO-TOP, that can be read using gensim in python.
- presto_top_model_annotations.xlsx contains annotations for the sub-cluster motifs (S1 File in the paper).
- mibig_gbk_2.0_clusterfile_ipresto_output_visualisation.html contains the visualisation of all MIBiG BGCs queried to the set of sub-clusters generated in this study.
Contents:
- antismashdb_dataset_tokenised_bgcs_clusterfile.csv contains the pre-processed BGCs (tokenised and filtered) from the antiSMASH-DB dataset. Genes are separated by commas and domains by semicolons.
- Pfam_100subs_tc.hmm is the unpressed Pfam database, additionally containing subPfam HMMs for the 112 most important biosynthetic Pfams.
- PRESTO-STAT_subclusters.txt contains all sub-clusters found by PRESTO-STAT applied to the antiSMASH-DB dataset.
- lda_model and files with lda_model* are the LDA model trained and used by PRESTO-TOP, that can be read using gensim in python.
- presto_top_model_annotations.xlsx contains annotations for the sub-cluster motifs (S1 File in the paper).
- mibig_gbk_2.0_clusterfile_ipresto_output_visualisation.html contains the visualisation of all MIBiG BGCs queried to the set of sub-clusters generated in this study.
| Date made available | 2 Aug 2022 |
|---|---|
| Publisher | Wageningen University & Research |
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iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures
Louwen, J. J. R., Kautsar, S. A., van der Burg, S., Medema, M. H. & van der Hooft, J. J. J., 9 Feb 2023, In: PLoS Computational Biology. 19, 2, p. e1010462Research output: Contribution to journal › Article › Academic › peer-review
Open Access3 Citations (Scopus) -
iPRESTO: integrated Prediction and Rigorous Exploration of biosynthetic Sub-clusters Tool
Louwen, J. J. R., Kautsar, S. A., van der Burg, S., Medema, M. H. & van der Hooft, J. J. J., 2022Research output: Non-textual form › Software
Open Access