Feature parameters

Bring up the GeneFinder menu (under the GeneFind.. button) and select [Feature Parameters]. Change the parameters to the ones given below and press the OK button.

Each Genefinder Feature is given a score. Click on an ATG, splice donor (Splice5) or splice acceptor (Splice3) and look at the blue information bar at the top of the screen to see the score. The Feature parameters are the minimum score for a feature to be included on the fmap.

The score of genefinder features is calculated from weight matrices (ATG, donor and acceptor) and codon usage tables in the wgf/ directory of ACEDB

To recalculate the GeneFinder Features click on the GeneFind.. button with the left mouse button OR bring up the GeneFinder menu with the right mouse button and select [GeneFinder Features]. Note there are fewer splice sites marked on the fmap.

The GeneFinder Features used for the last gene prediction are still highlighted in green. Press the Clear button at the top of the screen, otherwise GeneFinder will only use these features and subsequently find the same gene.

Choose the [AutoFind Gene] option from the GeneFinder menu and press Continue when the dialogue box appears. The old temp_gene is overwritten with a new prediction (see below).

Go to Step 3


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