Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.

摘要: Transposable elements (TEs) are ubiquitous components of eukaryotic genomes that impact many aspects genome function. TE detection in genomic sequences is typically performed using similarity searches against a set reference built from previously identified TEs. Here, we demonstrate this process can be improved by designing sets incorporate key the structure and evolution TEs combining these with Repbase Update (RU), which composed mainly consensus sequences. Using Arabidopsis as test case, our approach leads to an extra 12.4% These correspond novel fragments well extension already detected RU. Significantly, find could readily optimized only two sets, one containing true other mosaic capture structural diversity copies within family.