Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites

BMC Evolutionary Biology

Ralph A Dean¹  Joshua K Sailsbery² 

[1] Centennial Campus, Center for Integrated Fungal Research, North Carolina State University, 851 Main Campus Drive, Suite 233, Raleigh, NC, 27606, USA;Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA

关键词: Variable sites;    Conserved sites;    Discerning sites;    HMM;    Environmental sequencing;    Fungi;    Animals;    Plants;    Classification;    Discriminant analysis;    bHLH;   

Others  :  1140436
DOI  :  10.1186/1471-2148-12-154

 received in 2012-01-03, accepted in 2012-07-26,  发布年份 2012

【 摘 要 】

Background

The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi.

Results

Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites.

Conclusions

We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample.

【 授权许可】

   
2012 Sailsbery and Dean; licensee BioMed Central Ltd.

【 图 表 】

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