Gene Finding – DNA Finder

This method, located in the More Methods section, finds DNA regions which match those in the sequence file(s) you specify. GeneQuest uses the selected files to search both the top and bottom strands of your sequence.

To apply the method:

1. Double click on the method name (Gene Finding – DNA Finder) in the Method Curtain to open the Add Sequences dialog.

2. Locate and select the appropriate sequence files. Note that you may select multiple sequences, and of a variety of file types, including Lasergene .seq files, Lasergene project files from SeqBuilder Pro or GeneQuest, FASTA files, ABI or SCF trace files, SFF flowgram files, Phred files .phd), zip archives, DNA Multi-Seq Files (.mseq), and File of Filenames (.fof). Click Done.

The top and bottom strand for each sequence you selected will now appear in the Method Curtain below the Gene Finding method. If you selected multiple sequences, a Composite top and bottom strand will also be listed. The Composite strands are created by superimposing all of the top/bottom strands for your specified sequences.

A hit is recorded when the match reaches or exceeds the minimum match size parameter (see below). Gap characters are not inserted in the identical region to extend an alignment. With this method, you can locate multiple matches for a sequence, as long as the areas are at least as long as the minimum match size.

The score printed on the region plot indicates how many bases in the two sequences matched up. Using the Zoom In palette tool, zoom in until you see the numbers. Clicking once on the plot and holding the mouse button reveals the matching coordinates of the two sequence stretches and tells whether the match occurred on the top or bottom strand (see Customize the look of the Assay Document). If you wish to see the residues for the match, continue using the Zoom In tool until the sequence is displayed.

To change method parameters:

1. Double click on the Gene Finding 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 bases required to define a match. Note that GeneQuest will not accept a value less than 12 for this parameter.

3. To choose different files, click Set Data File to return to the Add Sequences dialog.