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Import/Export of variant monomers from Fasta/Sequence #2015

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olganaz opened this issue Jun 20, 2024 · 3 comments · Fixed by #2227
Closed

Import/Export of variant monomers from Fasta/Sequence #2015

olganaz opened this issue Jun 20, 2024 · 3 comments · Fixed by #2227
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@olganaz
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olganaz commented Jun 20, 2024

Background
Sometimes users need to register oligonucleotides containing randomized or "mixed" bases. It means that on the defined position a variant monomer could occur.
Variant monomer is a monomer which can be used instead of another monomer within listed variants.

Requirements
In addition to the requirements for import/export Sequences #1426 and Fasta #1755 the following symbols should be supported for:

  • RNA and DNA

If one of the following base symbols is entered (first column), this means that the base in the nucleotide can be represented by any of the bases indicated in the second column (in equimolar ratio)

  • Peptide monomers
    When importing X should be interpreted as variant monomer which could be any of unmodified peptide monomer X={A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y}
    When exporting symbol 'X' could be used both for variant monomers and for peptide monomers with natural analogue 'X'
@ljubica-milovic
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In addition to X as a symbol that represents "any amino acid", following symbols for Peptides should be supported:

Symbol Symbols of amino acid represented by it
B D, N
J L, I
Z E, Q

@ljubica-milovic
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By X (any amino acid), in addition to the 20 amino acids listed above two more are to be added to the list.
X =
[ A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y
and
O, U]

@AlexeyGirin
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Verified with issues.

Versions

  • Ketcher Version 2.25.0-rc.1 Build at 2024-09-03; 15:31:03
  • Indigo Toolkit Version 1.24.0-rc.1.0-gb8f099851-wasm32-wasm-clang-19.0.0
  • Chrome Version 128.0.6613.114 (Official Build) (64-bit)
  • Win10

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4 participants