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Here,I am giving an example. I am trying to compare two sequences sequence1.fa and sequence2.fa.
`sequence1.fa`
>sequence1
VKPFQTDALVITPGQTTNVLFTANASTNVGAVQQFFIAARPFVTGGGTFDNSTVAGIMSYNISNSNNSSS
…
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Hello,
I'm trying out Ribotin to assemble some tangles. They are probably not rRNA but I assume that it doesn't really matter. The morph size appears to be around 3 kbp.
```
ribotin-ref --appro…
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Greetings team! We are using foldseek for clustering on a batch of pdbs without aa sequence. We set the alignment-mode to `3di-alignment`. But the result still shows that the pdbs in one cluster have…
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Dear HDBSCAN developpers,
I'm a physicist using the HDBSCAN algorithm to analyze experimental results (I'm therefore not specialized in clustering!). It works quite well on my data, but I have the …
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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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UCLUST/USEARCH cluster slowly at identities far from 0.97 (i.e. the 0.60 setting used for prefiltering with open-ref OTU picking). Currently, the pick_open_reference_otus.py script does a prefilter at…
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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, I am trying to run isONclust2 first for isONcorrect, but I got this error for all the batches, one example:
Loaded input batch from batches/isONbatch_9.cer:
Batch number: 9
Bat…
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If you have own unpublished sequence data or data from other repositories not included in PrimerMiner, the should be an option to add your own sequences manually before clustering (in fasta format)
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Vsearch seems to never detect chimera with default parameters.
I think it lies on the fact that sequences are not dereplicated and therefore do not have a "count" section in fasta header.
However…