Coding Prediction – Starts Stops ORFs

One way to locate potential coding regions is to identify and to apply Open Reading Frame (ORF) plots for all six reading frames to your sequence. Although only a subset of ORFs are genuine coding regions, knowing their locations is a helpful adjunct to application of the more powerful methods of gene finding.

*Note: ORF detection can also be done in SeqBuilder Pro, our modern application that is installed alongside GeneQuest. To learn about finding and displaying ORFs in SeqBuilder Pro, click here.

The Coding Prediction – Starts Stops ORFs method, located in the More Methods section, predicts coding regions in the traditional way, by locating start codons and stop codons. The region between these codons is defined as the open reading frame (ORF). Results are presented as a series of region plots for each reading frame. Plots for starts, stops and ORFs are displayed individually. You can help define the boundaries of coding regions by displaying this method alongside (i) Borodovsky peaks for each frame and (ii) (in eukaryotes) candidate splice sites (see Patterns – Matrix).

Start and stop codons are determined by the active genetic code. Before applying the Coding Prediction > Starts Stops ORFs method to your sequence, you may select the appropriate code from the Options > Genetic Codes list. The code can be edited, if necessary, by selecting Options > Edit Selected Code.

If you choose to display an ORF region plot (a type of graph with bars representing “yes” areas and lines representing “no” areas), the plot will not include the terminator. If you select the ORF using the range selector, however, the terminator is added, making GeneQuest consistent with NCBI and with other Lasergene applications. If you wish, you may observe the terminator portion by making the selection, then using the Zoom In palette tool.

To change method parameters:

1. Double click on the method name in the Method Curtain; or select the method display and then Analysis > Method Parameters.

2. Specify the Minimum ORF Length, the minimum number of codons required to call a region an ORF. The shortest exons rarely fall under 25 codons (75 nucleotides).

3. Decide whether or not to check ORFs Must have a Start Codon.
   
   
   • When checked, this forces GeneQuest to begin an ORF with a start codon and end with a stop codon.
     
     
   • When unchecked, an ORF begins immediately after a stop and runs until the next stop codon, assuming there are at least 75 bp between stops.

To generate a summary table of codon usage for any selected segment of the sequence, which may also be useful in identifying coding regions, choose Analysis > Codon Usage.

To investigate further, consider using the Borodovsky method for evaluating coding potential.