Find Sequence

Choosing Select... Sequence... opens an interface for specifying an amino acid and/or nucleotide sequence; a similar interface is included in the Sequence Panel.

There are two sections arranged as index cards; clicking the tab for a card brings it to the front.

The Subsequence section allows the sequence to be specified as a string of one-letter codes. Case is not important. Ambiguity codes may be used:
- none - only allow exact matches of one-letter codes
- protein - in addition to exact one-letter code matching, allow B to match aspartic acid (D) and asparagine (N) and Z to match glutamic acid (E) and glutamine (Q)
- nucleic acid - in addition to exact one-letter code matching, allow R to match the standard purine nucleotides (A, G), Y to match the standard pyrimidine nucleotides (C, T, U), and N to match any of the five (A, C, G, T, U)
The PROSITE pattern section allows the sequence to be specified with PROSITE pattern syntax. Residue codes must be capitalized; extended syntax involving an asterisk, e.g. <{C}*>, is not supported.

Note that occurrences in all sequence types (protein, DNA, and RNA) will be considered matches unless the option to Force interpretation... as protein or nucleic acid sequence is on. When the option is on, only sequences of the indicated type will be examined for matches.