Table 1 Bit encodings for all nucleotide and amino acid symbols, and the number of bitwise operations required to check for equality when used as a query symbol
From: An optimized FM-index library for nucleotide and amino acid search
Bit encoding | Symbol group | # Bitwise Ops for comparison | |
|---|---|---|---|
Nucleotide IUPAC code | |||
A | 110 | 1 | 1 |
G | 101 | ||
C | 011 | ||
T | 001 | 2 | 2 |
X | 010 | ||
$ | 100 | ||
Amino acid IUPAC code | |||
A | 01100 | 1 | 2 |
D | 00011 | ||
E | 00110 | ||
G | 11010 | ||
I | 11001 | ||
K | 11001 | ||
L | 11100 | ||
P | 01001 | ||
R | 10011 | ||
S | 01010 | ||
T | 00101 | ||
V | 10110 | ||
C | 10111 | 2 | 3 |
F | 11110 | ||
H | 11011 | ||
M | 11101 | ||
N | 01000 | ||
Q | 00100 | ||
W | 00001 | ||
Y | 00010 | ||
X | 11111 | 3 | 3 |
$ | 00000 | ||