Trait-to-gene: a computational method for predicting the function of uncharacterized genes.

Journal Article (Journal Article)

The function of unknown genes is often inferred from comparisons to well-characterized homologs. In this paper, we show that, even if all of the homologs of a gene are unannotated, its function may be deduced through phylogenetic profiling. We have designed a series of algorithms that make functional predictions of genes based on orthology and set theory, but our approach to predicting gene function requires no previous knowledge of homolog function. With this technique, we successfully identified 94% of the clusters of orthologous groups that are known to be involved in flagella development or function. As a test, we removed the function of three putative flagellar genes that had been previously uncharacterized in Bacillus subtilis. We observed a motility phenotype for two of these three genes. Thus, these algorithms allow for high-throughput functional prediction of genes beyond that provided by simple orthology-based annotation endeavors.

Full Text

Duke Authors

Cited Authors

  • Levesque, M; Shasha, D; Kim, W; Surette, MG; Benfey, PN

Published Date

  • January 2003

Published In

Volume / Issue

  • 13 / 2

Start / End Page

  • 129 - 133

PubMed ID

  • 12546786

Electronic International Standard Serial Number (EISSN)

  • 1879-0445

International Standard Serial Number (ISSN)

  • 0960-9822

Digital Object Identifier (DOI)

  • 10.1016/s0960-9822(03)00009-5


  • eng