Predicting subcellular location of apoptosis proteins based on wavelet transform and support vector machine.
Apoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. As a result of genome and other sequencing projects, the gap between the number of known apoptosis protein sequences and the number of known apoptosis protein structures is widening rapidly. Because of this extremely unbalanced state, it would be worthwhile to develop a fast and reliable method to identify their subcellular locations so as to gain better insight into their biological functions. In view of this, a new method, in which the support vector machine combines with discrete wavelet transform, has been developed to predict the subcellular location of apoptosis proteins. The results obtained by the jackknife test were quite promising, and indicated that the proposed method can remarkably improve the prediction accuracy of subcellular locations, and might also become a useful high-throughput tool in characterizing other attributes of proteins, such as enzyme class, membrane protein type, and nuclear receptor subfamily according to their sequences.
Qiu
Jian-Ding
JD
Department of Chemistry, Nanchang University, 330031, Nanchang, People's Republic of China. jdqiu@ncu.edu.cn
Luo
San-Hua
SH
Huang
Jian-Hua
JH
Sun
Xing-Yu
XY
Liang
Ru-Ping
RP
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D051017:Apoptosis Regulatory Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005103:Expert Systems; D057166:High-Throughput Screening Assays; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D021381:Protein Transport; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013347:Subcellular Fractions / Q000378:metabolism
D000596:Amino Acids; D051017:Apoptosis Regulatory Proteins