Gene Finding – Protein Finder

This method, located in the More Methods section, finds protein regions which can code for a given Lasergene format protein sequence. GeneQuest uses the file you select to search all six reading frames of the nucleotide sequence.

To apply the method:

1. Double click on the method name in the Method Curtain to open the Protein Sequence dialog.

2. Locate the appropriate sequence file and highlight it. Acceptable sequence formats are Lasergene protein files (.pro) or text files (.txt).

3. Click Open.

A hit is recorded when the match reaches or exceeds the minimum match size parameter. Gap characters are not inserted to extend an alignment. With this method, you can locate multiple potential coding areas for a specified sequence, as long as the areas are at least as long as the minimum match size. This method can help locate introns and exons within a stretch of DNA.

The score printed on the region plot indicates how many nucleotides matched the protein. Use the Zoom In tool to enlarge the display until you see the numbers. If you want to know more about a particular match, select it using the object or range selector and continue to hold down the mouse button. GeneQuest will display the matching coordinates of gene and protein, the reading frame of the match, and the twenty residues at the 5’ and 3’ ends (see Customize the Display).

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 Match Size, the minimum number of identical codons required to define a match.

3. To choose a different file, click Set Data File to return to the Protein Sequence dialog.