Nature Reviews Genetics 7, 130-141 (February 2006) | doi:10.1038/nrg1769

Towards multidimensional genome annotation

Jennifer L. Reed1, Iman Famili2, Ines Thiele1 & Bernhard O. Palsson1  About the authors


Our information about the gene content of organisms continues to grow as more genomes are sequenced and gene products are characterized. Sequence-based annotation efforts have led to a list of cellular components, which can be thought of as a one-dimensional annotation. With growing information about component interactions, facilitated by the advancement of various high-throughput technologies, systemic, or two-dimensional, annotations can be generated. Knowledge about the physical arrangement of chromosomes will lead to a three-dimensional spatial annotation of the genome and a fourth dimension of annotation will arise from the study of changes in genome sequences that occur during adaptive evolution. Here we discuss all four levels of genome annotation, with specific emphasis on two-dimensional annotation methods.

Author affiliations

  1. Department of Bioengineering, University of California, San Diego, La Jolla, California, 92093, USA.
  2. Genomatica Inc., 5405 Morehouse Drive, Suite 210, San Diego, California 92121, USA.

Correspondence to: Bernhard O. Palsson1 Email:


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