Fig. 1

Example of how extrinsic evidence in form of spliced alignments from homologous proteins (blue) or RNA-seq reads (red) is used to determine scores for the support of a transcript (green). Likely exon-intron borders are inferred from the alignments to create intron hints. The start and stop codons of the protein alignments are used to create start and stop codon hints, respectively. The transcript scores utilize them to quantify the support of the transcript structure