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Pyl Peptide is changed to wrong letter while we save one to Fasta or Sequence file #4362

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NadezhdaPeskun opened this issue Mar 28, 2024 · 1 comment
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FASTA Bucket: FASTA related issues Priority: High

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@NadezhdaPeskun
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NadezhdaPeskun commented Mar 28, 2024

Steps to Reproduce

  1. Macro
  2. Peptides >> Add Pyl
  3. Save as Fasta and Sequence files

Actual behavior.
Pyl Peptide is shown as O letter while exporting to FASTA and Sequence.
image

Expected behavior
Pyl Peptide is shown as K letter while exporting to FASTA and Sequence.
As per @olganaz - Pyl belongs to K natural group so it should be represented as K letter in FASTA and Sequence
Please see comment from Olga below
image

Environment details:
Ketcher Version 2.20.0-rc.2 Build at 2024-03-27; 08:30:51
Indigo Toolkit Version 1.19.0-rc.2.0-g6c0e3fecf-x86_64-linux-gnu-11.2.1
Win10
Chrome Version 122.0.6261.129 (Official Build) (64-bit)

Related issues:

@NadezhdaPeskun NadezhdaPeskun added bug Priority: High FASTA Bucket: FASTA related issues labels Mar 28, 2024
@NadezhdaPeskun NadezhdaPeskun changed the title **Pyl** Peptide is changed to wrong letter while we save one to Fasta or Sequence file Pyl Peptide is changed to wrong letter while we save one to Fasta or Sequence file Mar 28, 2024
@NadezhdaPeskun NadezhdaPeskun added this to the Waiting for triage milestone Mar 28, 2024
@olganaz
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olganaz commented Apr 8, 2024

Various sources disagree on whether the symbol "O" is permissible in the FASTA format (https://en.wikipedia.org/wiki/FASTA_format VS https://zhanggroup.org/FASTA/). According to the IUPAC nomenclature, the symbol "O" is used to denote pyrrolysine. However, widely used tools by biologists such as BLAST and Uniprot generate an error when attempting to input an amino acid sequence containing the symbol "O". Therefore, it has been decided to support the import of the symbol "O", but when exporting, interpret it as the natural analog of pyrrolysine - "K" (lysine)

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Labels
FASTA Bucket: FASTA related issues Priority: High
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