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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

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