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Hello,
I've tried to annotate genome with both RNASeq and proteins database. For certain genomes it worked but for some others it failed with similar errors as described in #582 and #577 (see logs …
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Change sentence template for protein domain sentence from "Is predicted to encode a protein with the following domains:" to
"Is predicted to encode a protein with the following domain(s):" to indica…
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**Describe the bug**
Hi, I am using platon version 1.7 installed through mamba. As input I am using draft assmblies obtained from bacterial whole genome sequencing (enterobacteria, mainly klebsiella)…
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Dear TIES developers,
I would like to setup some FEP simulations for a protein-peptide system where I mutate a residue of the peptide. This seems similar to TIES-PM (https://doi.org/10.1021/acs.jct…
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I'm trying to use [HuggingFace's ESMFold](https://huggingface.co/facebook/esmfold_v1) to predict 3D protein structures from the protein sequence. I've got a PDB output that loads just fine on the [RCS…
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Something I noticed in our production server timeline. A user has successfully edited a sample sheet, but them clicking on "finish sheet editing" to return to browsing mode and saving a sheet version …
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Per issue #172, there is a request to restore the computationally predicted compound-to-protein edges (from ChEMBL) in RTX-KG2, that got dropped in KG2.6.0 when we deprecated all the old API-based RTX…
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Hello,
Thank you again for your help in my previous issue. I can finally run the ProtST task on my cluster using one GPU. However, I need clarification about the command that you provided.
I wan…
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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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Hi,
I have been wondering, how does funannotate deal with gene duplications when supplying protein evidence? Ive noticed that diamond doesn't seem to allow multi mapping and therefore only one of the…