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Thank you for the great tool! I'm trying to apply it to a large dataset of 97 samples and >3,000 proteins. However, it seems to indefinitely hang up at the following step:
[1] "Features with less tha…
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- [x] Read IsoGlyP paper
- [x] Review the portal and code
- [x] Review Seun' work and run the script
- [ ] Prepare a dataset + BCO
- [ ] Draw mockups to show the data
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Hello, recently i want to make some tests on your code, where can I get the large dataset containing 19,704 proteins mentioned in the paper? Thanks so much.
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Hi Vini,
I think the last patch of metaphor may have introduced the following issue:
Analyzing assembly
Skipping gene prediction
using protein fasta file: output/annotation/prodigal/c…
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Hi,
I want to know if foldseek can output multiple structural alignment generated using 3Di as aligned 3Di alphabet sequences in Fasta format and not aligned amino acid sequences of the proteins.…
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Hi,
I wonder what configuration and object looked like for these objects? https://cells.ucsc.edu/?ds=multimodal-pbmc+sct
We have a gene expression + CITE-seq data for several objects, and we'd lik…
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Hello. Thank you for making this great tool open-source. Is support for other types of molecules besides proteins on the roadmap for FoldSeek's development?
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Currently have the % of shared residues and % of shared proteins between CATH superfamilies and Pfam Clans, and CATH superfamilies and Pfam families.
One example of these results is for `http://daw…
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- [x] populate membranes with proteins that have defined `TM-Section` material
- [x] move linearly through verts
- [ ] move randomly through verts
- [ ] move through faces
- [ ] filter by face normals…
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I'm trying to cluster a set of ~500 conformations of the same protein but no matter what I try I only get 1 cluster.
Do I need to do something to the set of structures before clustering them?
I'…