Henry Hung-Yung Wang wrote:
> 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);
What's your regexp to split.
split //, $dna uses the last regexp used in the program.
Perhaps you meant split /\w/, $dna ?!
> foreach $bp (0..$#dna-8){
> $eightmer=join ('', @dna[$bp, $bp+1, $bp+2, $bp+3, $bp+4, $bp+5, $bp+6,
> $bp+7]);
Well, thats strange.
It is simplier written as:
$eightmer = join ('', @dna[$bp .. $bp+7]);
> if ($eightmer=~ $motif[0]){
> print "This sequence, $eightmer, is palindromic\n\n";
> } else {
> print "There is no other palindromic sequences\n\n";
> exit;
You exit whole the foreach loop when the FIRST NON-Palindromic sequence
is found.
> }
> }
>
> 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.
>
Greetings,
Andrea
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