Influence of e-value cutoff on transcript annotation rate. (a-d) Number of annotated transcripts (y-axis, log scale) by cut-off e-value plotted against sequence length (x-axis log scale). The total number of transcripts is shown in green, and the subset of annotated transcripts is shown in red. The number of transcripts with an annotation increases with the length of transcripts. The percentage of annotated transcripts depends on the cutoff e-value threshold. For example, an annotation of 50% of transcripts at 290 bp is reached at a cutoff of e-10 (a), this length increases to 680 bp when a cutoff of e-100 is used (d). We selected the minimum sequence length of 400 bp for our assembly to achieve a sufficient annotation rate of assembled sequences.
Looso et al. Genome Biology 2013 14:R16 doi:10.1186/gb-2013-14-2-r16