HIV Databases HIV Databases home HIV Databases home
HIV sequence database

Codes and Symbols in Sequence Alignments

This page decodes the symbols you may find in your sequences and alignments. We also provide a Codon Table for translating nucleotides into amino acids.

Symbols in Sequences

Symbol       Meaning
#            frameshift
?            position where no majority-rule consensus could be made
X            amino acid position where an IUPAC nucleotide prevented translation
*            stop codon
$            stop codon


IUPAC Nucleotide Ambiguity Codes

Symbol       Meaning      Nucleic Acid
A            A           Adenine
C            C           Cytosine
G            G           Guanine
T            T           Thymine
U            U           Uracil
M          A or C
R          A or G
W          A or T
S          C or G
Y          C or T
K          G or T
V        A or C or G
H        A or C or T
D        A or G or T
B        C or G or T
X      G or A or T or C
N      G or A or T or C


Cornish-Bowden (1985) IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE. Nucl. Acids Res. 13: 3021-3030.


last modified: Tue Feb 10 12:41 2009

Questions or comments? Contact us at

Operated by Triad National Security, LLC for the U.S. Department of Energy's National Nuclear Security Administration
© Copyright Triad National Security, LLC. All Rights Reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health