That "genes define proteins" has been a central tenet of molecular genetics for decades, but recent studies are sharply revising this simple picture. In particular, less than 2% of human DNA encodes proteins, yet we now know that the majority of DNA is transcribed into RNA, and there is a rapidly growing body of evidence that a significant portion of this noncoding RNA performs diverse, sophisticated and vital functions, especially in early development and in neurons. Conservation of a molecular sequence over the course ofevolution (as evidenced by its presence with little change across multiple species) is a key piece of evidence for its functional importance. Identifying such sequences is a much more difficult problem for RNA than for DNA. We have developed computationally intensive but powerful new algorithms for this task, and are applying them widely in both bacterial and vertebrate genomes. Thousands of candidate noncoding RNA genes have been discovered by these searches. Collaborators have already experimentally determined the functions of many of the bacterial examples. Some of them may prove to be good targets for novel classes of antibotics.