NucleicAcids
Type definitions
BiologicalSymbols provides two types of NucleicAcid:
| Type | Meaning |
|---|---|
DNA |
DNA nucleotide |
RNA |
RNA nucleotide |
The set of nucleotide symbols in BiologicalSymbols.jl covers the IUPAC nucleotides as well as a GAP (-) symbol.
| Symbol | Constant | Meaning |
|---|---|---|
| 'A' | DNA_A / RNA_A |
A; Adenine |
| 'C' | DNA_C / RNA_C |
C; Cytosine |
| 'G' | DNA_G / RNA_G |
G; Guanine |
| 'T' | DNA_T |
T; Thymine (DNA only) |
| 'U' | RNA_U |
U; Uracil (RNA only) |
| 'M' | DNA_M / RNA_M |
A or C |
| 'R' | DNA_R / RNA_R |
A or G |
| 'W' | DNA_W / RNA_W |
A or T/U |
| 'S' | DNA_S / RNA_S |
C or G |
| 'Y' | DNA_Y / RNA_Y |
C or T/U |
| 'K' | DNA_K / RNA_K |
G or T/U |
| 'V' | DNA_V / RNA_V |
A or C or G; not T/U |
| 'H' | DNA_H / RNA_H |
A or C or T; not G |
| 'D' | DNA_D / RNA_D |
A or G or T/U; not C |
| 'B' | DNA_B / RNA_B |
C or G or T/U; not A |
| 'N' | DNA_N / RNA_N |
A or C or G or T/U |
| '-' | DNA_Gap / RNA_Gap |
Gap (none of the above) |
http://www.insdc.org/documents/feature_table.html#7.4.1
These are accessible as constants with DNA_ or RNA_ prefix:
julia> DNA_A DNA_A julia> DNA_T DNA_T julia> RNA_U RNA_U julia> DNA_Gap DNA_Gap julia> typeof(DNA_A) BiologicalSymbols.DNA julia> typeof(RNA_A) BiologicalSymbols.RNA
Symbols can be constructed by converting regular characters:
julia> convert(DNA, 'C') DNA_C julia> convert(DNA, 'C') === DNA_C true
Bit encoding
Every nucleotide is encoded using the lower 4 bits of a byte. An unambiguous nucleotide has only one set bit and the other bits are unset. The table below summarizes all unambiguous nucleotides and their corresponding bits. An ambiguous nucleotide is the bitwise OR of unambiguous nucleotides that the ambiguous nucleotide can take. For example, DNA_R (meaning the nucleotide is either DNA_A or DNA_G) is encoded as 0101 because 0101 is the bitwise OR of 0001 (DNA_A) and 0100 (DNA_G). The gap symbol is always 0000.
Amino Acids
Set of amino acid symbols also covers IUPAC amino acid symbols plus a gap symbol:
| Symbol | Constant | Meaning |
|---|---|---|
| 'A' | AA_A |
Alanine |
| 'R' | AA_R |
Arginine |
| 'N' | AA_N |
Asparagine |
| 'D' | AA_D |
Aspartic acid (Aspartate) |
| 'C' | AA_C |
Cysteine |
| 'Q' | AA_Q |
Glutamine |
| 'E' | AA_E |
Glutamic acid (Glutamate) |
| 'G' | AA_G |
Glycine |
| 'H' | AA_H |
Histidine |
| 'I' | AA_I |
Isoleucine |
| 'L' | AA_L |
Leucine |
| 'K' | AA_K |
Lysine |
| 'M' | AA_M |
Methionine |
| 'F' | AA_F |
Phenylalanine |
| 'P' | AA_P |
Proline |
| 'S' | AA_S |
Serine |
| 'T' | AA_T |
Threonine |
| 'W' | AA_W |
Tryptophan |
| 'Y' | AA_Y |
Tyrosine |
| 'V' | AA_V |
Valine |
| 'O' | AA_O |
Pyrrolysine |
| 'U' | AA_U |
Selenocysteine |
| 'B' | AA_B |
Aspartic acid or Asparagine |
| 'J' | AA_J |
Leucine or Isoleucine |
| 'Z' | AA_Z |
Glutamine or Glutamic acid |
| 'X' | AA_X |
Any amino acid |
| '*' | AA_Term |
Termination codon |
| '-' | AA_Gap |
Gap (none of the above) |
http://www.insdc.org/documents/feature_table.html#7.4.3
Symbols are accessible as constants with AA_ prefix:
julia> AA_A AA_A julia> AA_Q AA_Q julia> AA_Term AA_Term julia> typeof(AA_A) BiologicalSymbols.AminoAcid
Symbols can be constructed by converting regular characters:
julia> convert(AminoAcid, 'A') AA_A julia> convert(AminoAcid, 'P') === AA_P true
Functions
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