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**Graph visualization**
- extend functionality based on JSON dependency
- generalize functions for diprotic and triprotic amino acids
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Hi,
I'd like to have terms to represent indels at the protein level (or please indicate what we should be using).
Right now at the transcript level there are:
-- conservative_inframe_insertion
-- d…
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Hi, thank you for your great job!
But I have a question about the number of indices missing values for certain amino acids.
According to your description in the paper, there are 13 discarded indi…
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Would everyone be ok if I were to run through the psi-mod CV and put in appropriate links to the amino acids modified? For instance, right now, MOD:01356 is_a MOD:00916 (modified serine), when I wou…
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Hi,
Thank you for developing NeuralPlexer. We ran our first attempts on a very challenging protein and we obtained promising results, most of all very different from the (useless) ones obtained wit…
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Some genetic codes such as the Vertebrate Mitochondrial Code allow potentially different start codons / start amino acids. Is it possible to take this into account in diamond, e.g. by specifying that …
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By default, MAFFT automatically determines whether a user has provided amino acid sequences or nucleotide sequences. Sometimes, MAFFT mistakes protein sequences for DNA sequences if a protein has many…
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Thanks for an excellent package.
My issue is as above. Certain amino acid sequences simply crash with an error of type
`[1] 132848 segmentation fault (core dumped) ./derna -i ~/test.fasta -o o…
h-ahl updated
3 weeks ago
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I would like to understand the difference between this term:
GO:1990928 response to amino acid starvation/ cellular response to amino acid starvation
Definition
Any process that results in a cha…
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Related to #20 and the issues mentioned in there, I would suggest to extend ModelCIF to capture all new types of quality estimates introduced with AlphaFold 3 (AF3). I also had a look at RoseTTAFold-A…