How do I search for Open Reading Frames?

Choose Analyze | Open Reading Frames.
Select the start/stop codons check box.
Specify the minimum amino acid length that you will consider to be a valid open reading frame in the min. # of amino acids text box. TIP: The majority of proteins are larger than 75 amino acids. However, eukaryotic exons can be as small as 20 to 25 amino acids.
Select check boxes for treating the sequence ends as start and stop codons. The options are: 5' ends are starts, 3' ends are stops, codons after stops are starts. Normally you would want all three boxes checked, because MacVector defines an open reading frame as a region flanked by a start codon and a stop codon. If your sequence fragment lies in the middle of a coding region and contains no start or stop codons, for example, MacVector will not report any open reading frames unless you have checked both 5' ends are starts codon and 3' ends are stops.The codons after stops are starts option is recommended for eukaryote sequences where introns are common. Where there are internal coding exons, it finds that the longest possible ORFs, ensuring that the entire exon is captured.
Select the genetic code that contains the start and stop codons you want to use from the genetic code drop-down menu.
You can restrict the search to a certain region of the sequence by typing in the sequence numbers that bracket the region in the Region panel, or by selecting a region from the features table pop-up menu at the right of the text boxes.
You can restrict the analysis to one or both strands, by selecting the appropriate item from the strand drop-down menu.
Select OK to perform the analysis.

How do I search for Open Reading Frames?

Related Topics.