TY - GEN
T1 - Protein remote homology detection using order profiles
AU - Liu, Bin
AU - Lin, Lei
AU - Wang, Xiaolong
AU - Wang, Xuan
PY - 2009
Y1 - 2009
N2 - Protein remote homology detection is a central problem in bioinformatics. In this study, we present a novel building block of proteins called order profiles (OP) to use the evolutionary information of the protein sequence frequency profiles and apply this novel building block to remote homology detection. Order profiles contain the evolutionary information extracted from the protein sequence frequency profiles outputted by PSI-BLAST. The performance of our method is further improved by applying an efficient feature extraction algorithm from natural language processing, namely, latent semantic analysis (LSA). When tested on SCOP 1.53 benchmark, our method outperforms the other building-block-based methods and related methods.
AB - Protein remote homology detection is a central problem in bioinformatics. In this study, we present a novel building block of proteins called order profiles (OP) to use the evolutionary information of the protein sequence frequency profiles and apply this novel building block to remote homology detection. Order profiles contain the evolutionary information extracted from the protein sequence frequency profiles outputted by PSI-BLAST. The performance of our method is further improved by applying an efficient feature extraction algorithm from natural language processing, namely, latent semantic analysis (LSA). When tested on SCOP 1.53 benchmark, our method outperforms the other building-block-based methods and related methods.
KW - Latent semantic analysis
KW - Profiles
KW - Remote homology detection
KW - Support vector machine
UR - http://www.scopus.com/inward/record.url?scp=70450152077&partnerID=8YFLogxK
U2 - 10.1109/IJCBS.2009.53
DO - 10.1109/IJCBS.2009.53
M3 - Conference contribution
AN - SCOPUS:70450152077
SN - 9780769537399
T3 - Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
SP - 255
EP - 260
BT - Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
T2 - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
Y2 - 3 August 2009 through 5 August 2009
ER -