Symbols
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 |
Amino Acid Codes
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 |
Nucleotide Codes
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 |