Figure 3

Transcripts predicted in a region of S. cerevisiae chr IV (strain S288c) comprised between ~270.600 bp and ~319,000 bp. From top to bottom: coverage on the forward strand, coverage on the reverse strand, genes (protein-encoding regions) (Genes), reconstruction of the transcripts obtained with ORA (ORA) and with Cufflinks (Cufflinks). In the row reporting the predictions of ORA, the introns are colored in red. Red numbers indicate key differences in transcript reconstruction between the two software: (1) transcripts formed by multiple “blocks” in the reconstruction with Cufflinks which are determined by the presence of gaps with no coverage in the coding region, (2) adjacent genes joined in polycistronic transcripts by Cufflinks despite large coverage differences.