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Workflow
The search engine definitely plays the most important role in the peptide identification process. As illustrated below, what the search engine itself does is bascically first in silico diges…
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Hello @jarojasva!
While working on the database, I observed that some of the .fasta files containing amino acid sequences (such as Q6RXW0,Q6RXW1, Q6RXW2, Q6TMA3) reported in the tables 1_Aerobic_a…
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Hi Jason, maybe you can advise using something better than exonerate for protein2genome mapping, but... since I am using it - I've found a very strange behavior of your perl script, I can't explain.
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Hi, Thanks for your nice pipeline!
ViWrap 1.2.1 is encountering an error while running the command
```
./ViWrap/ViWrap run --input_metagenome /P/release/C/1-5_assembly/final_assembly.fasta --inpu…
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Hi,
Recently I'm trying to use EVM to annotate my genome. Since I'm a freshman for gene structure annotation, I didn't get any alternative splicing events from the final GFF. I searched for the manua…
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Hi there,
Having set up `alphafold` in my machine (NVIDIA GeForce RTX 2080 GPU, ), which I've tested successfully, I'm now coming across the error below running it on a 5586 AA predicted protein (f…
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Hello,
From the example walkthroughs in this repo (`generate.ipynb`), it is clear how to generate sequence and structure form a prompt. Code from example below:
```
protein_prompt = ESMProtein(se…
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Hello.
Thanks for this amazing work.
I am trying to redesign a peptide binder while keeping the sequence at some positions.
For example, I would like to keep the prolines at positions 2,9 and 16 a…
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In the published models (especially those using the "European (P-gp modified, CYP3A4 36 h)" individual), I found some differences in the expression profiles from the values stored in the database.
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**Describe the bug**
This isn't a bug issue with the code, I just thought I'd point out there's a typo on the Prosit website. When identifying a file from which test spectra are generated, it says …