Hi everyone,
Thanks for the advice. They were really helpful. I have tried a different
way of approaching my problem and it's now working. However, I do
appreaciate all the suggestions that you have provided me.
Henry
On Mon, 12 Nov 2001, mark crowe (JIC) wrote:
> 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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