PATTERN-MATCHING SYNTAX
SymbolMatches Example
PatternResult
A,C,D,... Alanine, cysteine, aspartate,... 
 MAKSY
 Matches any sequence that contains MAKSY motif.
. any residue 
 MAK..SY
 Matches any sequence that contains MAK and SY motifs separated by exactly two residue.
[DEKR] any residue
from the list		 
 MAK[AG]SY
 Matches any sequence that contains MAK and SY motifs separated by either alanine or glycine.
[^DEKR] any residue
not in the list		 
 MAK[^AG]SY
 Matches any sequence that contains MAK and SY motifs separated by any residue other than alanine or glycine.
x? Matches 0 or 1 x's
where x is any of the above		 
 MAK.?SY
 Matches any sequence that contains MAK and SY motifs separated by 0 or 1 residue.
x* Matches 0 or more x's 
 MAK.*SY
 Matches any sequence that contains MAK and SY motifs separated by 0 or more residues.
x+ Matches 1 or more x's 
 MAK.+SY
 Matches any sequence that contains MAK and SY motifs separated by at least one residue.
x{m,n} Matches at least m
but no more than n x's		 
 MAKA{3,5}SY
 Matches any sequence that contains MAK and SY motifs separated by at least 3, but no more than 5 alanines.
^ Anchors the match to
the begining of the sequence		 
 ^MAKSY
 Matches any sequence starting with MAKSY
$ Anchors the match to
the end of the sequence		 
 ASCKA$
 Matches any sequence ending with ASCKA
NOTE: check any PERL manual for the full description of the pattern-matching
(also known as regular expression) syntax.