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Fig. 5 | Mobile DNA

Fig. 5

From: A beginner’s guide to manual curation of transposable elements

Fig. 5

Example of TE-Aid output. TE-AID produces a set of plots and graphical representations that helps understanding the nature of the query sequence. This example features the consensus sequence of a LTR/Gypsy element of the rice weevil Sitophilus oryzae. In all plots, the horizontal axis represents the length of the query sequence (6000 nt in this example). A Fragment and divergence plot. Each blastn hit retrieved from the genome is represented with a line. Red lines are hits regarded as “full-length” and by default > 90% of the query sequence. Location on the y axis represents the % divergence with respect to the query (the higher the divergence the more base changes there are); by default hits are plotted with some degree of transparency to identify highly represented fragments. B Coverage plot representing the depth of coverage from blastn hits for each section of the query. A height of 2500 over the first 500 bases of the 5’end indicates that on average ~ 2500 copies are found in the genome whose sequences are homologous to this section of the query. In this example, there are many more blastn hits of the LTR subparts than for the internal part of the LTRs, likely representing the high frequency of solo-LTRs in the genome. C Self-alignment dot-plot reveals repeated sequences in the query - see Protocol 14 for a full explanation. The LTR subparts can be identified as parallel lines in the top left and bottom right of the graph. D Graphical interpretation of the dot-plot (top) and representation of open reading frames (black lines) and structural TE protein hits. The LTR subparts are shown as light green arrows. The arrowheads (“> >”) in dark green represent micro-homology along the sequence, though not diagnostic for this family of TE. A single open reading frame (black box) has been found and the translated protein is homologous to a known LTR/Gypsy polyprotein (POL) gene (green box)

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