Skip to main content
Fig. 4 | BMC Genomics

Fig. 4

From: Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti

Fig. 4

Identification of proteins derived from mobile genetic elements using PIT. a Proportion of non-insect PIT hits (red) and PIT hits matching known Ae. aegypti genes (grey) that display >30% amino acid sequence similarity to known mosquito TEs (E-value <105) at increasing thresholds for % sequence coverage. Arrow indicates optimal threshold for TE identification, used for all remaining analyses unless otherwise specified. b As for (a), except that the proportion of PIT hits with >45% sequence coverage is plotted at different sequence similarity thresholds. c (i) Breakdown of the non-insect PIT proteome into virus-derived proteins, proteins with homology to known mosquito TEs (Additional file 4), and other non-classified proteins (other). Proteins with >95% amino acid homology and >95% sequence coverage were considered ‘exact matches’ to known TEs (Table 1). (ii) Identification of TEs in the Aedes PIT proteome. d as for (c), except only hits associated with two or more peptides were included in the analysis. e (i) Identification of TEs in the non-insect PIT hits using either TEfam, RepBase, or both databases as a reference. (ii) Identification of TEs in the Aedes PIT proteome using a combined TEfam and RepBase reference database

Back to article page