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MotifPrototyper: a Bayesian profile model for motif families.

ABSTRACT: In this article, we address the problem of modeling generic features of structurally but not textually related DNA motifs, that is, motifs whose consensus sequences are entirely different but nevertheless share "metasequence features" reflecting similarities in the DNA-binding domains of their associated protein recognizers. We present MotifPrototyper, a profile Bayesian model that can capture structural properties typical of particular families of motifs. Each family corresponds to transcription regulatory proteins with similar types of structural signatures in their DNA-binding domains. We show how to train MotifPrototypers from biologically identified motifs categorized according to the TRANSFAC categorization of transcription factors and present empirical results of motif classification, motif parameter estimation, and de novo motif detection by using the learned profile models.

SUBMITTER: Xing EP

PROVIDER: S-EPMC489970 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

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MotifPrototyper: a Bayesian profile model for motif families.

Xing Eric P EP Karp Richard M RM

Proceedings of the National Academy of Sciences of the United States of America 20040713 29

In this article, we address the problem of modeling generic features of structurally but not textually related DNA motifs, that is, motifs whose consensus sequences are entirely different but nevertheless share "metasequence features" reflecting similarities in the DNA-binding domains of their associated protein recognizers. We present MotifPrototyper, a profile Bayesian model that can capture structural properties typical of particular families of motifs. Each family corresponds to transcriptio ...[more]

PMID: 15252200

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