Motif search performs detection of specific sequence patterns
in database entries. These patterns (motifs) can be defined using degenerated bases
and/or regular expressions (see the rules for entering motifs).
Rules for entering motifs:
- Parentheses () enclose one or more symbols that can be repeated some number
of times.
- Braces {} enclose numbers that tell how many times the preceeding symbol or the symbols within the preceding parentheses
must be found. The two numbers, separated by a comma, specify a minimum and maximum number of repetitions. The numbers must be less than 65,536,
and the first must be less than or equal to the second. If the second number is omitted, but the comma is present, there is no upper limit; if the
second number and the comma are both omitted, the quantifier specifies an exact number of required matches.
- UIPAC symbols are supported (only uppercase letters are treated as UIPAC code):
| N = A or C or G or T |
|
| R = A or G (puRine) |
Y = C or T (pYrimidine) |
| B = C or G or T (not A) |
V = A or C or G (not T) |
| D = A or G or T (not C) |
H = A or C or T (not G) |
| K = G or T (Keto in large groove) |
M = A or C (aMino in large groove) |
| S = G or C (strong - 3H bonds) |
W = A or T (week - 2H bonds) |
- Examples:
GATA{5,} means GAT, followed by A repeated from 5 to 65,536 times
GAT(TG){0,4}R{3} means GAT, followed by TG repeated from 0 to 4 times, followed by exactly 3 purines
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