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What is reported in github is not pseudo-log-likelihood:
https://github.com/ntranoslab/esm-variants/blob/main/esm_variants_utils.py#L90
Pseudo-likelihood requires masking each position one-by-one,…
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Hi, Thank you for this great contribution to research. I have been experimenting various ways to create an immune age and found your paper recently. Could you please tell me which all immune proteins …
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Hi,
Thank you for creating a great platform to examine the CRISPR-Cas transposon systems bioinformatically!
I was able to follow along the tutorial to find CRISPR and Cas proteins in the genome o…
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Hi 👋! In the paper it is mentioned: "For DIPS, the split is based on protein family to separate similar proteins". Is there a source code for this split? I could only find a [random split in `parititi…
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Gene strand can be very useful to detect prophages, but it is currently lacking from the `.gb` files. Because of that, there's no way to benchmark a tool that leverages strandness using proteins/ORFs …
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Is there a way to prompt MM to report multiple protein link sites in the xl search output? When a peptide is present in two isoforms or in the rare event - present in two unrelated proteins - the prot…
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I am running the README.md steps on the Intel DevCloud. I generated full_under_200.txt both with the julia script get_proteins_under_200aa.jl and julia_get_proteins_under_200aa.ipynb for good measure.…
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Add a parser for the [BaliBASE 3](http://www-bio3d-igbmc.u-strasbg.fr/balibase) multiple alignment benchmark.
Reference:
Thompson JD1, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest developments of t…
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We would like chemical pages for reaction participants.
For example,
chemicals link to CHEBI. Instead we would like to link to a chemical page which list all of the genes + reactions that th…
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When aligning proteins with paralogs located in a cluster, `miniprot` produces alignments encompassing two or more distinct genes.
For example, aligning mouse protein NP_001036176.1 to human chrom…