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e-Genetics: gene discovery by structure

Discovering a gene can be extremely difficult if its sequence differs significantly from known genes. After all, most approaches depend on the assumption that the primary sequence of one gene strongly resembles that of another, known gene — what if it doesn't? On p. 1107, Junhyong Kim and John Carlson discuss a novel in silico approach — e-Genetics — that can search for related proteins on the basis of structural similarity. They have used e-Genetics to identify Drosophila odor and taste receptor families, which other strategies had failed to uncover. Both families are G-protein-coupled receptors (GPCRs); the authors therefore developed a way of mapping an n-dimensional protein space in which GPCRs occupy a particular region, using parameters such as the periodicity of hydrophobicity/polarity along the length of the protein. In tests on SWISS-PROT sequences, the algorithm correctly identified 96% of GPCRs and did not misclassify a single non-GPCR. Kim and Carlson propose that e-Genetics will be useful for discovering new GPCRs and could be modified to identify other proteins, such as ion channels and connexins.

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This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Search for Related Content Social Bookmarking                         What's this?