Introduces controlled variabilities into the search query.
Use this symbol: |
When you want to: |
Example |
Possible Answers |
. |
Translate to X for protein or enumerate to A, G, C, and T for nucleotide (generates four search terms). |
S.GKD |
SXGKD/SRGKD |
... |
Match any nucleotide\amino acid. |
S....GKD |
SXXXXGKD/SFTSYGKD |
[XYZ] |
Designate a set of possible nucleotide\amino acid character matches within the square brackets. |
[SG]XXXXGKD |
SXXXXGKD/GXXXXGKD |
^XYZ$ |
Search for the exact sequence XYZ. |
^SXXXXGKD$ |
SXXXXGKD |
{m,n} |
Designate a stretch (range) of X residues with at least m and maximum n length. |
SX{3,4}GKD |
SXXXGKD/SXXXXGKD |
{n} |
Designate a stretch (range) of X residues of exactly n length. |
SX{4}GKD |
SXXXXGKD |
Creates a positive scoring mismatch for amino acids (e.g., A sequence query with a B will retain the B, and the B will score positively against D or N in the hit subject sequence).
Use this symbol: |
When you want to search: |
Example |
Possible Answers |
X |
any amino acid |
LXRK |
Allows matching of any amino acid at the position of X. |
B |
D or N |
LBRK |
LDRK or LDNK |
Z |
E or Q |
LZRK |
LERK or LQRK |
J |
I or L |
LJRK |
LIRK or LLRK |
Generates multiple queries for nucleotides where the degenerate code is replaced by the nucleotides it represents.
Use this symbol: |
When you want to search: |
Example |
Possible Answers |
N |
A or C or G or T |
ACNT |
ACAT or ACCT or ACGT or ACTT |
R |
A or G |
ACRT |
ACAT or ACGT |
Y |
C or T |
ACYT |
ACCT or ACTT |
M |
A or C |
ACMT |
ACAT or ACCT |
K |
G or T |
ACKT |
ACGT or ACTT |
S |
C or G |
ACST |
ACCT or ACGT |
W |
A or T |
ACWT |
ACAT or ACTT |
H |
A or C or T |
ACHT |
ACAT or ACCT or ACTT |
B |
C or G or T |
ACBT |
ACCT or ACGT or ACTT |
V |
A or C or G |
ACVT |
ACAT or ACCT or ACGT |
D |
A or G or T |
ACDT |
ACAT or ACGT or ACTT |
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