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Figure 3 | Genome Biology

Figure 3

From: Reference based annotation with GeneMapper

Figure 3

Extrapolation in GeneMapper. Use of extrapolation to pinpoint the location of unmapped exons in the second stage of GeneMapper pipeline. The blue sequence shows the possible location of the unmapped exon in the target sequence, and we assume that the gene is in the same strand in both species. (a) If an unmapped exon has mapped exons both to its upstream as well as downstream, then the unmapped exon should be mapped between the orthologs of its nearest mapped upstream and downstream exons. (b) If only the exons upstream of an unmapped exon are mapped, then the unmapped exon should be mapped downstream of the ortholog of its closest mapped exon. (c) If only the exons downstream of an unmapped exon are mapped, then the unmapped exon should be mapped upstream of the ortholog of its closest mapped exon.

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