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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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### Description of feature
The first reasonable methods to predict antigen specificity emerge, e.g.
* ERGO-II (https://www.frontiersin.org/articles/10.3389/fimmu.2021.664514/full, https://github.c…
grst updated
3 months ago
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## Summary
There are a total of 31 V regions in the TCR Beta receptor locus. 11 of them are pseudogenes and 20 are transcribed genes (still need to confirm this). We only use primers for the 20 trans…
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We need to come up with appropriate test systems to evaluate the different methods.
The dataset should contain examples of:
- [ ] Identical sequences, different conformations
- [ ] Homologous s…
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1. Cluster input data at 30% similarity (eg., Uniref30 from colabfoldDB)
2. Split sequences from ProteinGym into two subgroups:
- Group 1: 10/87 sequences fully removed from training data clusters […
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**Configuration file:** nongithub.toml
**Description:** effusion, A method for predicting protein function, Effusion, that uses a sequence similarity network to add context for homology transfer, …
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Dear @yinlabniu,
Thank you again for a very important tool to annotate CAZymes and identify CGCs in the microbial genomes of interest.
I am interested in examining how complete are the CGCs in my …
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### What would you like to Propose?
~ Would like to add Damerau-levenshtein distance Algorithm in Dynamic Programming folder.
### Issue details
The Damerau–Levenshtein distance is a measure of th…
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## Short description of the problem
The `--min-alignment-fraction` parameter of `anvi-dereplicate-genomes` is not working as expected.
## anvi'o version
I'm using the master version as of thi…
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Dear all
Thanks for making this great tool available.
Maybe, I missed it in the documentation but I can't seem to find a description of how many mismatches you allow when trimming adapters.
So my…