lenti229 [~/perltest]>more regexp.pl
#!/opt/local/bin/perl -w
#  regexp.pl
#  example uses of regular expressions

# @protein contains test1.pep and test3.pep
$protein [0] = ">A28086  Length: 104";
$protein [1] =
"VKQIESKSAFQEVLDSAGDKLVVVDFSATWCGPCKMIKPFFHALSEKFNNVVFIEVDVDDCKDIAAECEVKCMPTFQFF
KKGQKVGEFSGANKEKLEATINELL";
$protein [2] = ">ORF15 S. aureus pathogenicity island";
$protein [3] =
"MEDVTNEEVFEMIDSRTGVLNANDWKSQLRRSATTQALKKTTTNAEIILCNDESLKGLVQYDAF
EKVTKLKRLPYWRSKGDTNYYWADIDTTHVISHIDKLYNVQFSRDLIDTVIEKEAYQNRFHPIKSMIESKSWDGIKRIET
LFIDYLGAEDNHYNREVTKKWMMGAVARIYQPGIKYDSMIILYGGQGVGKSTAVSKLGGHWYNQSIKTFKGDEVYKKLQG
SWICEIEELSAFQKSTIEDIKGFISAIVDIYRASYGKRTERHPRQCVFVGTTNNYEFLKDQTGNRRFFPITTDKNKATKS
PFDDLTPDVVQQMFAEAKVYFDEDPTDKALLLDKEASEMALKVQEAHSEKDALVGEIEEFLERPIPSDYWYRTLEEKRVS
AHDVIDQDYIKLYGDGKLIELPNTKPGAYVWRDKVCSMEIWKVMMKRDDQPQQHHLRKIDKALRNTNYCDTVKKQTRYGE
GIGKQYGFSVDLASYYKNLKV";

# regular expressions are found after ~= and between /  /
$i = 0;

while (defined($protein[$i]))  {

if ($protein[$i] =~ /CGPC/) {
    print "CGPC motif found in line $i.\n";
                            }
$i++;
                               }
#in regular expressions, ^ means start of line, $ means end of line
# . matches any character
# + match immediately preceding character one or more time
# * match immediately preceding character zero or more times
# ? match immediately preceding character zero or one times
# [  ] enclose a set of characters, match any one
# [^ ] enclose a set of characters, match everything except them
$i = 0;

while (defined($protein[$i])) {
if ($protein[$i] =~ /^>/)  {
    print "Line $i is a fasta ID line.\n";
                           }
if ($protein[$i] =~ /NELL$/)  {
    print "Line $i has a C-terminal NELL motif.\n";
                              }
# simple N-glycosylation: N X S or T  (sensitive, but not specific)
if ($protein[$i] =~ /N.[ST]/) {
    print "Line $i has a simple glycosylation motif.\n";
                              }
# PROSITE N-glycosylation: N, any residue except P, S or T, any except P
if ($protein[$i] =~ /N[^P][ST][^P]/) {
    print "Line $i has a PROSITE glycosylation motif.\n";
                                 }
# PROSITE thioredoxin motif (high sensitivity and specificity)
if ($protein[$i] =~
/[LIVMF][LIVMSTA].[LIVMFYC][FYWSTHE]..[FYWGTN]C[GATPLVE][PHYWSTA]C.{6}[LIVMFYWT]
/)
{
    print "Line $i has a PROSITE thioredoxin motif.\n";
}
$i++;
                              }
exit;

lenti230 [~/perltest]>perl regexp.pl
CGPC motif found in line 1.
Line 0 is a fasta ID line.
Line 1 has a C-terminal NELL motif.
Line 1 has a PROSITE thioredoxin motif.
Line 2 is a fasta ID line.
Line 3 has a simple glycosylation motif.
Line 3 has a PROSITE glycosylation motif.
lenti231 [~/perltest]>