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Title 

Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches

 

BLAST와 HMMER 결과로부터 기능적으로 동일한 단백질을 예측하는 알고리즘

Authors 

Dong Su YuDae Hee LeeSeong Keun KimC H LeeJ Y SongE B KongJihyun Kim

Publisher 

The Korean Society for Applied Microbiology

Issue Date 

2012

Citation 

Journal of Microbiology and Biotechnology, vol. 22, no. 8, pp. 1054-1058

Keywords 

Artificial neural networkBioinformaticsError back-propagation algorithmFunctionally equivalent proteinSequence-based method

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.

ISSN 

1017-7825

Link 

http://dx.doi.org/10.4014/jmb.1203.03050

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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