Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches = BLAST와 HMMER 결과로부터 기능적으로 동일한 단백질을 예측하는 알고리즘

Cited 6 time in scopus
Metadata Downloads
Title
Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches = BLAST와 HMMER 결과로부터 기능적으로 동일한 단백질을 예측하는 알고리즘
Author(s)
Dong Su Yu; Dae Hee LeeSeong Keun Kim; C H Lee; J Y Song; E B Kong; Jihyun Kim
Bibliographic Citation
Journal of Microbiology and Biotechnology, vol. 22, no. 8, pp. 1054-1058
Publication Year
2012
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.
Keyword
Artificial neural networkBioinformaticsError back-propagation algorithmFunctionally equivalent proteinSequence-based method
ISSN
1017-7825
Publisher
Korea Soc-Assoc-Inst
DOI
http://dx.doi.org/10.4014/jmb.1203.03050
Type
Article
Appears in Collections:
Synthetic Biology and Bioengineering Research Institute > Synthetic Biology Research Center > 1. Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.