Identify submitochondria and subchloroplast locations with pseudo amino acid composition: approach from the strategy of discrete wavelet transform feature extraction.
It is very challenging and complicated to predict protein locations at the sub-subcellular level. The key to enhancing the prediction quality for protein sub-subcellular locations is to grasp the core features of a protein that can discriminate among proteins with different subcompartment locations. In this study, a different formulation of pseudoamino acid composition by the approach of discrete wavelet transform feature extraction was developed to predict submitochondria and subchloroplast locations. As a result of jackknife cross-validation, with our method, it can efficiently distinguish mitochondrial proteins from chloroplast proteins with total accuracy of 98.8% and obtained a promising total accuracy of 93.38% for predicting submitochondria locations. Especially the predictive accuracy for mitochondrial outer membrane and chloroplast thylakoid lumen were 82.93% and 82.22%, respectively, showing an improvement of 4.88% and 27.22% when other existing methods were compared. The results indicated that the proposed method might be employed as a useful assistant technique for identifying sub-subcellular locations. We have implemented our algorithm as an online service called SubIdent (http://bioinfo.ncu.edu.cn/services.aspx).
Department of Chemistry, Nanchang University, Nanchang 330031, China; Department of Mathematics, Nanchang University, Nanchang 330031, China.
Shao-Ping
SP
Shi
Jian-Ding
JD
Qiu
Xing-Yu
XY
Sun
Jian-Hua
JH
Huang
Shu-Yun
SY
Huang
Sheng-Bao
SB
Suo
Ru-Ping
RP
Liang
Li
L
Zhang
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D001185:Artificial Intelligence; D002736:Chloroplasts / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D008928:Mitochondria / Q000737:chemistry*; D024101:Mitochondrial Proteins / Q000032:analysis*; D008954:Models, Biological; D010940:Plant Proteins / Q000032:analysis*; D010944:Plants / Q000737:chemistry; D058067:Wavelet Analysis
D000596:Amino Acids; D024101:Mitochondrial Proteins; D010940:Plant Proteins