Overview of repeat annotation and de novo repeat identification.

The availability of a large amount of genomic sequences has provided unique opportunities for understanding the composition and dynamics of transposable elements (TEs) in plants. As the cost of sequencing declines, the genomic sequences of most crop plants will be available within the next few years. Thus, the annotation of genomic sequences, rather than sequence availability, will become the "bottleneck" for genome study. Since TEs are the largest component of most plant genomes, the automation of TE identification and classification is essential for future genome annotation as well as characterization of TEs. In this chapter, the functions and mechanisms of different repeat finding tools are reviewed, with a focus on de novo repeat identification programs. In addition, this chapter covers the further processing of results from de novo identification programs and the construction of repeat libraries for downstream genome analyses.