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 dete...

Full description

Saved in:
Bibliographic Details
Published in:Journal of microbiology and biotechnology Vol. 22; no. 8; p. 1054
Main Authors: Yu, Dong Su, Lee, Dae-Hee, Kim, Seong Keun, Lee, Choong Hoon, Song, Ju Yeon, Kong, Eun Bae, Kim, Jihyun F
Format: Journal Article
Language:English
Published: Korea (South) 01.08.2012
Subjects:
Algorithms
Computational Biology - methods
Protein Structure, Tertiary
Proteins - genetics
Proteins - metabolism
Sequence Homology, Amino Acid
ISSN:1738-8872, 1738-8872
Online Access:Get more information
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1738-8872
1738-8872
DOI:10.4014/jmb.1203.03050