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There used to be a page about the Protein families game on the website, which is now missing.
Can you please add a new section 'Outreach' to the Help tab of the website that points to https://www.ebi…
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Hi，
When i use the gtdbtk-2.1.0/bin/python3.8 or gtdbtk-2.3.2/bin/python3.8 gtdbtk de_novo_wf --genome_dir /public/home/lcy/arc/soil4210 --archaea --outgroup_taxon p__Altiarchaeota --out_dir /public/…
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In 1.5 we had all mappings of Chembl targets to Chembl target components (and then to uniprot) in the default lens, regardless if it is a single protein or a complex or a family. With the IMS reload, …
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It might be a silly question but I still don‘t understand how you perform domain clustering by foldseek.
You mentioned in your nature article "Clustering predicted structures at the scale of the kno…
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If my protein does not belong to an explicit pfam family, how to generate a new sequence?
I guess: extract the closest pfam family(or several families) to fine-tuning the progen2 pretrained model, ri…
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Example from EMMAA covid model:
WARNING: [2021-08-17 14:29:41] indra.assemblers.pybel.assembler - Node should not have variants: bp(MESH:D019895 ! Transposases), [{'kind': 'hgvs', 'hgvs': 'p.?'}]
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I have run dbCAN3 for my fungal whole proteome data (and also for some other stain for this species) using HMMER, dbCAN_sub and DIAMOND tool. For the results, I kept those predicted by >=2 of these to…
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From a [curation report issue](https://github.com/wikipathways/wikipathways-help/issues/26), how to best model protein families in pathways. Either use Pfam id on a single node representing the protei…
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Any fix that could be recommended? It runs fine with 800 files
COMMAND:
`python corecruncher_master.py -in SA_proteins -out SA_proteins_out_80_100u -ref GCF_900475245.1_43024_E01_protein.faa -freq 8…
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[2024-10-28 04:01:14] INFO: GTDB-Tk v2.4.0
[2024-10-28 04:01:14] INFO: gtdbtk classify_wf --genome_dir new_genome_data/ --skip_ani_screen --out_dir classify_wf_out --cpus 16
[2024-10-28 04:01:14] IN…