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Currently, we use Nextclade to translate from nucleotides to amino acids.
We also use it to realign the notes and amino acids, even though our nucleotides are already aligned.
This seemed fine f…
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#### Current behavior:
45 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check|
…
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#### Current behavior:
40 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check|
…
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#### Current behavior:
40 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check|
…
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#### Current behavior:
40 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check |…
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#### Current behavior:
40 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check |
…
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50 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check |
|-------|-------------|---…
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#### Current behavior:
50 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check |…
-
50 genes are discovered to be uncorrelated with their corresponding reactions in `Transport reactions`.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually check |
|---------|-----------|---…
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As of now VespaG is not able to handle fasta files containing non-essential amino acids (e.g. U or O) or undetermined amino acids (X). Running `vespag predict` with such a fasta file will lead to a Va…