MotifPrototyper: a Bayesian profile model for motif families

Proceedings of the National Academy of Sciences of the United States of America
Eric P Xing, Richard M Karp

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.

References

Feb 4, 1994·Journal of Molecular Biology·A KroghD Haussler
Aug 1, 1996·Computer Applications in the Biosciences : CABIOS·K SjölanderD Haussler
May 15, 1998·Trends in Biochemical Sciences·G D Stormo, D S Fields
Dec 11, 1999·Nucleic Acids Research·E WingenderF Schacherer
Feb 12, 2002·Bioinformatics·Rachel KarchinDavid Haussler
Jul 24, 2004·Journal of Bioinformatics and Computational Biology·Eric P XingRichard M Karp

❮ Previous
Next ❯

Citations

Dec 2, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Man-Hung Eric TangOle Winther
Jun 6, 2009·Briefings in Functional Genomics & Proteomics·Leelavati Narlikar, Ivan Ovcharenko
Nov 4, 2005·Bioinformatics·Leelavati Narlikar, Alexander J Hartemink
May 6, 2011·Bioinformatics·Emi TanakaUri Keich
Jun 14, 2012·Nucleic Acids Research·Ting-Ying ChienDarby Tien-Hao Chang
Jun 29, 2010·BMC Bioinformatics·Matias PiipariTim Jp Hubbard
May 10, 2006·PLoS Computational Biology·Kenzie D MacIsaac, Ernest Fraenkel
Sep 28, 2006·PLoS Computational Biology·Thomas HamelryckAnders Krogh
Apr 3, 2007·PLoS Computational Biology·Shaun MahonyPanayiotis V Benos
Dec 12, 2007·PLoS Computational Biology·Edoardo M Airoldi
Jul 27, 2010·PLoS Computational Biology·Stephen F AltschulYi-Kuo Yu
Feb 9, 2012·PloS One·Chien-Yu ChenDarby Tien-Hao Chang
Dec 11, 2013·PloS One·Luis Carvalho
Apr 18, 2007·Proceedings of the National Academy of Sciences of the United States of America·Alexandre V Morozov, Eric D Siggia
Mar 26, 2014·Bioinformatics·Emi TanakaUri Keich
May 3, 2006·Current Opinion in Structural Biology·Mikhail S Gelfand
Sep 26, 2007·Genomics, Proteomics & Bioinformatics·Wei Wei, Xiao-Dan Yu

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.