Figure 5.

Example of alternatively spliced models built from short reads. The figure shows a capture of a 4 kb genomic region from V. vinifera chromosome 12 between 3,836,500 bp and 3,840,500 bp. The first track (Genoscope annotations) contains the automatic annotation from [44]. The green models are GeneWise alignments of Uniprot proteins. Alignment of V. vinifera cDNAs from [44] are in red, and public V. vinifera ESTs are in light green. The next track displays the models predicted by G-Mo.R-Se (untranslated region in grey, CDS in red). Initial covtigs are displayed as brown boxes (average depth of covtigs is written below each covtig). Alignments of velvet contigs are displayed in purple. Ab initio models produced by geneID [51] and SNAP [52] are displayed in blue and pink, respectively. The short reads coverage depth is plotted on the last track (black): the dashed red line shows the threshold used to build covtigs. Model M2 is confirmed by numerous resources, model M3 seems to be a minor alternative splice form (it is only supported by two public ESTs: E1 and E2), and model M1 is a novel alternative splice form.

Denoeud et al. Genome Biology 2008 9:R175   doi:10.1186/gb-2008-9-12-r175
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