Who's your neighbor? New computational approaches for functional genomics


Several recently developed computational approaches in comparative genomics go beyond sequence comparison. By analyzing phylogenetic profiles of protein families, domain fusions, gene adjacency in genomes, and expression patterns, these methods predict many functional interactions between proteins and help deduce specific functions for numerous proteins. Although some of the resultant predictions may not be highly specific, these developments herald a new era in genomics in which the benefits of comparative analysis of the rapidly growing collection of complete genomes will become increasingly obvious.

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Figure 1: Context-based approaches in comparative genomics.
Figure 2: Phylogenetic patterns, domain fusion, and gene clustering help predict functional pathways.


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We thank L. Aravind, Arcady Mushegian, and Yuri Wolf for numerous helpful discussions of the issues considered in this article, and Martijn Huynen and Peer Bork for sending us preprints of their publications.

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Correspondence to Eugene V. Koonin.

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Galperin, M., Koonin, E. Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol 18, 609–613 (2000). https://doi.org/10.1038/76443

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