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Hey! I'm very new to functional data, and have a naive question: can these methods be used to model longitudinal trajectories of discrete states? If not, are they other better methods for clustering t…
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## Expected Behavior
I am clustering billions of protein sequences. I already built the database. I was expecting linclust to run fairly quickly, but it seems to get stuck on the initial `kmermatcher…
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When clustering or searching with short sequences, obvious hits may be missed. This is also a problem when much of the sequences are masked. It is probably due to few distinct unmasked k-mers in the s…
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Dear all
We are currently testing AGNOSTOS on our system, but breaking it based on the different snakemake sub-runs in `agnostos-wf/db_update/rules/`
In the steps within mmseqs_clustering_update…
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It seems that in AptaCluster, you are performing clustering with the entire DNA sequences. In RNA aptamers, the DNA sequences contains T7 promoter which will not appear in RNA aptamer molecules. So I …
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Thanks for the amazing tool!
The viral DNA code is very dynamic and has no repair mechanisms, therefore viruses quickly mutate. However, they should be conserved on the aminoacid level, because de…
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Dear Sir,
I used 64 CPUs and provided 2TB of memory to run BiG-SCAPE-1.1.5, for clustering 140,000 BGCs. However, I encountered the following error: OSError: [Errno 12] Cannot allocate memory. The c…
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Hi @martin-steinegger ,
Thank you for the awesome software for structure-based clustering and sequence search. I was wondering if its possible to run the `easy-search` or `easy-cluster `commands wi…
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- [ ] Datasets
- [ ] AlphaFold 3 PDB dataset
- [x] PDB mmCIF filtering script (`scripts/filter_pdb_mmcifs.py`)
- [x] Fix periodic residue count-chemical component coun…
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Hi all,
There was a recent [question posted to the QIIME forum](https://forum.qiime2.org/t/vsearch-de-novo-output-uc-option/16697) that got me thinking about why the results might differ between ru…