PMC

An example where the option ‘ignore conflicts with other strand’ helps. The lines in (a) show two nested Drosophila genes as annotated in FlyBase (). The nine-exon gene on the forward strand includes a two-exon gene on the reverse strand within a long intron. The lines in (b) show the prediction with the default parameters. The gene on the forward strand is split into two genes by introducing two very short false positive exons so that the three predicted genes do not overlap. The lines in (c) show the prediction with the option ‘ignore conflicts with other strand’, which is identical to the annotation except for a short missed exon. This graphic has been obtained using gff2ps () from http://genome.imim.es/software/gfftools/GFF2PS.html.