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I am currently trying to obtain residue embeddings for protein sequences. The typical workflow involves the following steps:
```
protein = ESMProtein(sequence=sequence)
protein_tensor = self.mode…
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Hello!
I'm having a slight issue with the annotations generated by EGAPx. When I translate the CDS into a protein sequence, I'm seeing a lot of premature stop codons. This is a species where I am s…
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**Steps to reproduce:**
1. Open the Colab example from the README.
2. Run the provided script.
3. Observe the `FileNotFoundError` due to the missing `example_seqs.fasta` file.
**Request:**
Co…
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For a homodimeric protein with two identical sequences A and B, how can we export the intra-subunit crosslinks (A,A) and inter-subunit crosslinks (A, B)? I can only export intra-subunit crosslinks (A,…
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We have download many metagenome fastq files and need to align them to a custom protein database for calculating CPMs. We use 'kaliisto index --aa' command to build index from our FASTA-file contain…
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I have briefly used Gradio before and could have an attempt at designing a frontend for the project. However, before starting, I wanted to discuss how much feature parity we could achieve with DeepMin…
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Hi, thanks for creating this tool. But recently when I use pepquery2 in web application and stand alone version, there was error about the mgf file in s3 bucket is not exist. I attached the screenshot…
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Add an option to convert DNA sequences into their protein counter parts. This can be coupled with the option of specifying which codon position is the first nucloetide and also position of introns.
A…
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dear all,
I've found the site to compare the protein sequences :
https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi.
it's about comparing every protein sequence to the PSSM Database with RPS…
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* **ARBA rule (ID and label):**
ARBA00028584
* **Sequences with problematic annotation (ID + gene/protein name):**
https://www.pombase.org/gene/SPAC1296.04
* **Description of issue**
…