Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches

Dong Su Yu, Dae Hee Lee, Seong Keun Kim, Choong Hoon Lee, Ju Yeon Song, Eun Bae Kong, Jihyun F. Kim

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1054-1058
Number of pages5
JournalJournal of microbiology and biotechnology
Issue number8
Publication statusPublished - 2012 Aug

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Applied Microbiology and Biotechnology


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