Bring up the GeneFinder menu (under the GeneFind.. button) and select
[AutoFind Parameters]. Change the parameters to the ones given below
and press the OK button.
AutoFind parameters are weights and limits which are used by the
GeneFinder algorithm to predict a gene. AutoFind parameters can be
varied by the user, which allows GeneFinder to be tuned to find genes
typical of a particular organism; in this case Schizosaccharomyces
pombe
AutoFind parameters are:
[Aside: the additional cost is added above 100 bp (given a minimum
intron length of 30 bp). This is hard coded in ACEDB 4.1 (and has been
modified for this database) but will
become an AutoFind parameter in the next release. The additional cost
is the log of the additional length over 100bp multiplied by the
weight "intron rate per log bp".]
min intron length
min exon length does not apply to the first and last exon
intron cost the cost to the gene score for including each
intron
intron rate per log bp an additional cost for including an
intron above a certain length is added according to this weight (see Aside)
coding:intron score ratio the coding score is derived from
a codon usage table and visualised on the fmap as blocks of coding
potential. The coding score is increased proportionately by this
weight.
Press the Clear button to remove the green highlighting of GeneFinder
features and then select [AutoFind Gene] under the GeneFind.. menu.
Press Continue in the dialouge box which appears. The temp_gene
is overwritten. Note that the GeneFinder prediction exactly matches
the gene specified in the EMBL record. Double click the text
EM:D13249 to the left of the scale and inspect the full text of the
EMBL record. You will see that the intron/exon structure has been
confirmed experimentally.
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