Mining “junk” DNA to find hidden transcriptional gems

The genome is rich in information, posing analysis and visualization challenges, while offering enticing opportunities to discover functional structures. Interestingly, half the human genome is routinely discarded from most analyses as ldquojunkrdquo DNA, when interspersed repeats are masked. The GESTALT Workbench is an online tool for large-scale genomic sequence analysis and visualization, emphasizing the interpretation of interspersed repeats. Using GESTALT's new modular structure, author implemented dynamic and automated analysis pipelines, including the FEAST suite of algorithms. FEAST quantifies ldquotranscriptional footprintsrdquo leading to the computational identification of large numbers of transcripts lacking exon conservation and apparently not coding for proteins.