<![CDATA[
#!perl -w
use strict;
# testing chapter 2 ideas
#
# count the stars in $sky
my $sky = "***************";
my $cnt = $sky =~ tr/*/*/;
print "Stars in the sky: $cnt\n";
# dna sequence with *
my $seq = "";
foreach ( qw/TAG**CAT*GCGC*ATAA
GGCCGGCCAGGTCCA/ ) {
print "Sequence: $_\n";
# count the nucleotides in $_
$cnt = tr/GC//;
print "Count of gc: $cnt\t(", int(($cnt/length)*100), "%)\n";
$cnt = tr/AT//;
print "Count of at: $cnt\t(", int(($cnt/length)*100), "%)\n";
# canonicalize to lower case
($seq = $_) =~ tr/A-Z/a-z/;
print "Lower case: $seq\n";
# count the stars in $_
$cnt = tr/*/*/;
print "Count of stars: $cnt\n";
# change non-alphas to single space
($seq = $_) =~ tr/a-zA-Z/ /cs;
print "New sequence: $seq\n";
# bookkeeper -> bokeper
($seq = $_) =~ tr/a-zA-Z//s;
print "New sequence: $seq\n";
}
# cold-blooded, egg-laying vertebrates
# class Reptilia, ie snake, lizard,
# crocodile, turtle, or dinosaur, ...
my $HOST;
my $host = "Reptilian";
($HOST = $host) =~ tr/a-z/A-Z/;
print "The $HOST or the $host is similar\n";
$seq = "";
# dna sequence with N, and ambiguous codes
foreach ( qw/TAGYNCASWTNGRCGCNATAA
NGGKNCMGCBSGGTWCA/ ) {
print "Sequence:\t$_\n";
($seq = $_) =~ tr/ATGCYRSWKMBDHVN/TACGRYSWMKVHDBN/;
print "Complement:\t$seq\n";
$seq = reverse $seq;
print "Reversed:\t", $seq, "\n";
}
__END__
tr/ATGCYRSWKMBDHVN/TACGRYSWMKVHDBN/;
Base Name Bases Represented Complementary Base
A Adenine A T
T Thymidine T A
U Uridine(RNA only) U A
G Guanidine G C
C Cytidine C G
Y pYrimidine C T R
R puRine A G Y
S Strong(3Hbonds) G C S*
W Weak(2Hbonds) A T W*
K Keto T/U G M
M aMino A C K
B not A C G T V
D not C A G T H
H not G A C T D
V not T/U A C G B
N Unknown A C G T N
]]>