Hi Henry
Have you looked at using substr to take each octamer from the start for the
sequence? It's probably a lot more efficient than splitting it into an array
and taking the first 8 bases each time (althought I'm pretty sure that was
exactly the way I did my first DNA scripts too :-)
Also, if it's any use to you, here is my reverse complement subroutine,
which you could use as the basis of a palindrome checker which tests for any
palindrome, rather than just the restricted set you are using (of course,
those may be all the ones that you're interested in).
sub complement {
# Reverse complements the supplied string
my $seq = shift; # Get the string
$seq = reverse $seq; # Reverse it (scalar, therefore character reverse)
# Complement each base (IUPAC codes, upper and lower case)
$seq =~ tr/GATCgatcRYMKrymkSWswHBVDhbvdNn/CTAGctagYRMKyrmkWSwsDVBHdvbhNn/;
return $seq;
}
Cheers
Mark C
> -----Original Message-----
> From: Henry Hung-Yung Wang [mailto:[EMAIL PROTECTED]]
> Sent: 09 November 2001 15:31
> To: [EMAIL PROTECTED]
> Subject: simple code
>
>
>
> Hi All,
>
> I have just written some codes, but they are not doing what I
> wanted them
> to do. Here are the codes:
>
> @motif= ('ACGTACGT', 'AAAATTTT', 'CCGGCCGG', 'GGCCGGCC');
>
> print "Please enter sequences to be examined:\n\n";
> $dna=<STDIN>; chomp $dna;
>
> @dna=split (//, $dna);
> foreach $bp (0..$#dna-8){
> $eightmer=join ('', @dna[$bp, $bp+1, $bp+2, $bp+3, $bp+4,
> $bp+5, $bp+6,
> $bp+7]);
> if ($eightmer=~ $motif[0]){
> print "This sequence, $eightmer, is palindromic\n\n";
> } else {
> print "There is no other palindromic sequences\n\n";
> exit;
> }
> }
>
> I am trying to take the input and make them into sequences of
> 8 letters.
> Then I want to match the sequences with the 'motif' defined
> in the codes.
> However, when I run the program, the only motif that was
> recognized was
> 'AAAATTTT'. What am I doing wrong here? Thanks for the help.
>
> Henry
>
>
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