Import/Export of variant monomers from Fasta/Sequence

[olganaz]

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]

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]

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]

Verified with issues.

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