Pattern definition


b) Pattern definition

You can define a pattern according to PERL regular expressions. These examples refer to a simple four-residue pattern:

Pattern to be searched Identified sequences
First positionSecond positionThird positionFourth position
G[IL]KP G I or LKP
G.KP Gany amino acidKP
G[^L]KP Gany amino acid except LKP

Advanced features for pattern definition:
The star symbol "*" means a repetition (zero or more times) of the previous symbol.
The plus symbol "+" means a repetition (one or more times) of the previous symbol.
Example: the pattern GK.*HA identifies segments consisting of GK and HA spaced by an undefined number of amino acids.

Parentheses ( ) can be used to group a sequence and apply a rule to the group.
You can specify how many repetition you are searching for by using a pair of curly braces { } with one or two numbers inside.
Example: the pattern (PQV){3,5} identifies the following sequences:
PQVPQVPQV - that is, the pattern PQV repeated 3 times;
PQVPQVPQVPQV - that is, the pattern PQV repeated 4 times;
PQVPQVPQVPQVPQV - that is, the pattern PQV repeated 5 times;
You can leave not specified the lower or the upper number or repetition.
Example: (PQV){2,} identifies any repetition of PQV (two or more times).


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