Test cases from Gremme et al. 2005

GeneSeqer GenomeThreader (w/out intron cutout) GenomeThreader (with intron cutout)
total output gsq-OSchr10.out9 gth-OSchr10.out9 gth-OSchr10-IC.out9
parameter settings parameters.gsq parameters.gth parameters.IC.gth
alignments the same struct_same.gsq struct_same.gth *
struct_same.IC.gsq * struct_same.IC.gth
alignments similar, but on opposite strands strand_diff.gsq strand_diff.gth *
gene structures differ, but at same locus struct_diff.gsq struct_diff.gth *
struct_diff.IC.gsq * struct_diff.IC.gth
cDNA maps to different locus locus_diff.gsq locus_diff.gth *

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