#Genetic codes and residues

The reference data the deck reads, all exported. Runnable tour: jennifer run examples/tables.j.

#Genetic codes

Nine NCBI genetic codes, each a map of string to string from DNA codon to one-letter residue, stop as *:

Ids 7 and 8 were retired, so walk codonTableIds() rather than a range. An unknown id raises.

bioseq.STANDARD["ATG"];             # "M"
bioseq.codonTable(2)["AGA"];        # "*"
bioseq.codonTableName(2);           # "Vertebrate Mitochondrial"
bioseq.codonTableIds();             # [1, 2, 3, 4, 5, 6, 9, 10, 11]

#Differences from the standard code

The test suite restates these lists independently of the generator.

NCBI marks CGA and CGC as absent in code 3 rather than arginine. A map cannot express "absent", so they are kept as R; a sequence that depends on the distinction needs a hand check.

#Start codons

bioseq.startCodons(1);    # ["TTG", "CTG", "ATG"]
bioseq.startCodons(11);   # ["TTG", "CTG", "ATT", "ATC", "ATA", "ATG", "GTG"]

This is why orfsWith takes a table id rather than a codon map.

#IUPAC ambiguity codes

bioseq.expandIupac("R");            # "AG"
bioseq.iupacClass("R");             # "[AG]"
bioseq.matchesIupac("R", "G");      # true
bioseq.matchesIupac("A", "N");      # false - one-way

IUPAC_DNA and IUPAC_RNA map each code to the bases it admits; A, C, G, T/U map to themselves. Lookups take any case; a non-IUPAC character raises.

iupacClass renders a code as a regex character class for your own patterns; findIupac does not use it.

COMPLEMENT_DNA and COMPLEMENT_RNA cover the whole alphabet. Codes complement as sets (R to Y, B to V); S, W and N map to themselves. Complementing twice returns the original.

#Residue properties

def k as bioseq.AminoAcid init bioseq.aminoAcid("K");
$k.three;        # "Lys"
$k.name;         # "Lysine"
$k.monoMass;     # 128.09496
$k.avgMass;      # 128.1741
$k.pKa;          # 10.8
$k.charge;       # 1
$k.hydropathy;   # -3.9

aminoAcid takes a one- or three-letter code in any case ("k", "Lys"). aminoAcids() returns 22 records: the twenty standard residues in three-letter alphabetical order (ARNDCEQGHILKMFPSTWYV), then selenocysteine (U) and pyrrolysine (O). Masses are residue masses (free amino acid less one water). pKa is the EMBOSS iep side-chain value, 0.0 for a side chain that does not ionise.

B, Z, X, J and * have no record, since they have no single mass or pKa; aminoAcid raises on them and hasAminoAcid is the guard.

Asserted in the test suite:

• Leucine and isoleucine have identical mass (mass spectrometry reports "Leu/Ile").
• Glycine is the lightest residue.
• Monoisotopic mass is below average mass for every residue except selenocysteine, because selenium's most abundant isotope is heavier than its average.
• A side chain has a charge exactly when it has a pKa: H, K, R basic; C, D, E, Y acidic.

THREE_LETTER maps the whole protein alphabet, ambiguity codes (Asx, Glx, Xaa, Xle) and stop (Ter) included, to three-letter codes; oneToThree reads it.

#Parameter constants

#How the data is maintained

src/topics/tabledata.j is generated by tools/gentables.j. The generator writes each alternative code as the standard code plus its documented reassignments, and before emitting asserts that BLOSUM62 is symmetric across all 576 pairs, that ten known matrix values are right, and that every residue's identity score beats all nineteen of its substitutions. See Design notes.