You can want to add 'M' and '_' in parens to capture in one shot or concatanate 'M'.$1.'_' depending of what you want to do.
One way to do it:
#!/usr/bin/perl -w
use strict;
my $seqnum=1;
while (my $seq=<DATA>) {
chomp $seq;
print "sequence #",$seqnum++,":\n";
while ($seq =~ /M([GAVLIFWPSTCYNQDEKRH]+)_/g) {
print "\t",$1,"\n";
# or: print "\t","M${1}_","\n";
}
}
__DATA__
MHGRRRRRRRRRRRRRRRRRRRRRRRRRRRRRD_MHGRRRRRRRRD_
CMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVTECMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVT
AWPPPPPPPPPPPPPPPPPPPPPPPPPPPPP_LNAWPPPPPPPPPPPPPPPPPPPPPPPPPPPPP_L
FOOBARMNOTTHISONE_XYZMTHISYES_MTHISNOT_
|