Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Algorithm for Predicting Functionally Equivalent Proteins from BLAST and HMMER Searches

  • Yu, Dong Su (Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Dae-Hee (Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Seong Keun (Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Choong Hoon (Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Song, Ju Yeon (Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kong, Eun Bae (Department of Computer Science and Engineering, Chungnam National University) ;
  • Kim, Jihyun F. (Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology)
  • Received : 2012.03.21
  • Accepted : 2012.04.01
  • Published : 2012.08.28
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Abstract

In order to predict biologically significant attributes such as function from protein sequences, searching against large databases for homologous proteins is a common practice. In particular, BLAST and HMMER are widely used in a variety of biological fields. However, sequence-homologous proteins determined by BLAST and proteins having the same domains predicted by HMMER are not always functionally equivalent, even though their sequences are aligning with high similarity. Thus, accurate assignment of functionally equivalent proteins from aligned sequences remains a challenge in bioinformatics. We have developed the FEP-BH algorithm to predict functionally equivalent proteins from protein-protein pairs identified by BLAST and from protein-domain pairs predicted by HMMER. When examined against domain classes of the Pfam-A seed database, FEP-BH showed 71.53% accuracy, whereas BLAST and HMMER were 57.72% and 36.62%, respectively. We expect that the FEP-BH algorithm will be effective in predicting functionally equivalent proteins from BLAST and HMMER outputs and will also suit biologists who want to search out functionally equivalent proteins from among sequence-homologous proteins.

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