AutoFind Parameters

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:

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.

[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".]

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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