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).