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

by borisz (Canon)
on Jul 10, 2005 at 11:10 UTC ( [id://473750]=note: print w/replies, xml ) Need Help??


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), $/;     
   }
}

[download]
Boris

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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]
      -3 since the position is after ATG. $/ is just the newline for the print statement.
      Boris
[reply]
[d/l]
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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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