Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches.
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, sequencehomologous 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.
Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea.
Dong Su
DS
Yu
Dae-Hee
DH
Lee
Seong Keun
SK
Kim
Choong Hoon
CH
Lee
Ju Yeon
JY
Song
Eun Bae
EB
Kong
Jihyun F
JF
Kim
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000235:genetics* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
D011506:Proteins