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Transposable elements (TEs), or transposons, form a major fraction of the eukaryotic genome (Kidwell and Lisch 2001). Dismissed for some time as junk DNA, these repetitive sequences are now recognized for their diverse evolutionary roles. In this issue of Genome Research, Bao and Eddy (2002) describe a software tool (RECON) for de novo annotation of transposons in genomic sequence, offering new possibilities for discovery to biologists interested in TE evolution as well as a practical tool for masking repetitive DNA from genomic annotation pipelines. In this commentary, I begin by reviewing why transposons are relevant to studies of genome evolution. I then outline the advances of Bao and Eddy’s method from previous work, highlighting certain exemplary features of the RECON method. Finally I describe some of the open questions of transposable element evolution that may be more easily addressed by large-scale bioinformatics and functional genomics approaches as RECON, and more tools like it, become available.

Transcendent Elements: Whole-Genome Transposon Screens and Open Evolutionary Questions