Motivation: It is currently believed that the human genome contains about twice as much non-coding functional regions as it does protein-coding genes, yet our understanding of these regions is very limited.

Results: We examine the intersection between syntenically conserved sequences in the human, mouse and rat genomes, and sequence similarities within the human genome itself, in search of families of non-protein-coding elements. For this purpose we develop a graph theoretic clustering algorithm, akin to the highly successful methods used in elucidating protein sequence family relationships.

The algorithm is applied to a highly filtered set of about 700 000 human–rodent evolutionarily conserved regions, not resembling any known coding sequence, which encompasses 3.7% of the human genome. From these, we obtain roughly 12 000 non-singleton clusters, dense in significant sequence similarities. Further analysis of genomic location, evidence of transcription and RNA secondary structure reveals many clusters to be significantly homogeneous in one or more characteristics. This subset of the highly conserved non-protein-coding elements in the human genome thus contains rich family-like structures, which merit in-depth analysis.

Availability: Supplementary material to this work is available at http://www.soe.ucsc.edu/~jill/dark.html

To whom correspondence should be addressed.

Author notes

1Center for Biomolecular Science and Engineering, Baskin School of Engineering University of California in Santa Cruz, 1156 High Street, Santa Cruz, CA 95064;, 2Howard, USA Hughes Medical Institute, and 3McGill Center for Bioinformatics, School of Computer Science, McGill University Street, 3775 University, Montreal, QC, Canada, H3A 2B4