use strict;
my $str = 'NM_12345.5:c.1999+500C>A
NR_12345.5:c.1999+500C>A
XM_12345.5:c.1999+500C>A
XR_12345.5:c.1999+500C>A
ENST12334455677:c.1999+500C>A';
my $regex = qr/(?P<reference_sequence>(NM|NR|XM|XR)_[0-9]{4,12}|ENST[0-9]{1,11})(\.(?P<version>([0-9]?[0-9])))?(:(?P<prefix>c|n)\.(?P<start>-?[1-9][0-9]{0,7})(?P<start_offset>[+-][1-9][0-9]{0,7})?(?P<ref>[ACTG])>(?P<alt>[ACTG]))?/mp;
if ( $str =~ /$regex/g ) {
print "Whole match is ${^MATCH} and its start/end positions can be obtained via \$-[0] and \$+[0]\n";
# print "Capture Group 1 is $1 and its start/end positions can be obtained via \$-[1] and \$+[1]\n";
# print "Capture Group 2 is $2 ... and so on\n";
}
# ${^POSTMATCH} and ${^PREMATCH} are also available with the use of '/p'
# Named capture groups can be called via $+{name}
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html