Re: extracting open reading frame (ORF) from a FASTA file

in reply to extracting open reading frame (ORF) from a FASTA file

local $_  = $your_input_string;
while ( /ATG/g ) {
   my $start = pos() - 3;
   if ( /T(?:AA|AG|GA)/g ) {
     my $stop = pos;
     print $start, " ", $stop, " ", $stop - $start, " ", 
       substr ($_, $start, $stop - $start), $/;     
   }
}
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Boris

Comment on Re: extracting open reading frame (ORF) from a FASTA file Download Code

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Re^2: extracting open reading frame (ORF) from a FASTA file by Nadiah (Novice) on Jul 12, 2005 at 07:28 UTC
Hi Boris, about ur codes right.. may i know what this line means and why do we need to minus 3? my $start = pos() - 3; secondly, substr ($_, $start, $stop - $start), $/;	[reply]
Re^3: extracting open reading frame (ORF) from a FASTA file by borisz (Canon) on Jul 12, 2005 at 07:42 UTC
`-3` since the position is after ATG. `$/` is just the newline for the `print` statement. Boris	[reply] [d/l] [select]
Re^2: extracting open reading frame (ORF) from a FASTA file by Nadiah (Novice) on Jul 12, 2005 at 08:01 UTC
Hi Boris, Thanks for your help.. but I need further explainations on the codings. About the codes right.. may i know what this line means and why do we need to minus the pos() by 3? my $start = pos() - 3; Secondly, why is there a need for this substr statement? substr ($_, $start, $stop - $start), $/;	[reply]

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