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Hi,
Thanks for the amazing resource! I have backbone structures (from RFdiffusion that consist only of glycin) and I used ProteinMPNN to put a sequence into the backbones. It would be useful to pre…
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Hello,
I've got a question regarding the argument `--maxaccepts` of the `vsearch` command `--cluster_fast`:
The manpage states the following about `maxaccepts`:
"_The search process sorts tar…
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Hi,
I was checking ESM-3 structure embedding, and ESM-3 sequence embedding, and found that the distance between embeddings is very less ( 0.0001) . I am curious how ESM-3 model is pre-trained with …
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When you run easy search and output the pident/fident columns, is this sequence similarity (what you would get from mmseqs2/blast) or structure-sequence similarity (using the 3Di)?
Also, how can I …
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dev 1.11.3 bio 2.1.11 helm 2.1.1
Data: [sample_FASTA](https://dev.datagrok.ai/f/System.AppData/Bio/samples/sample_FASTA.csv)
To reproduce:
1. Delete some values in the Sequence column.
2. Go to B…
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Hi all, I was thinking that it would be useful to provide a sequence similarity metric to enable comparing protein or DNA sequences. The metric could compute all-by-all similarities or even employ som…
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Compute pairwise protein sequence similarity scores fir each functional pair
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I.e. in when clustering TCRs on amino-acid similarity it might be nice to return a string that encapsulates the conserved sequence, with a wild-card character (maybe %D:N, for example suggesting that …
n-hal updated
1 month ago
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I have a set of nucleotide sequences and I need the pairwise sequence similarity of all vs all.
I understand that one should create a fake_pref and use it to run mmseqs align. Yet, in the document…
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When uploading something that contains sequences, they should be compared for duplication or similarity with existing sequences, and the user should be given an option to consolidate/remap