title: jEcho: an evolved weight vector to characterize the protein's post-translational modification motifs.
abstract: Protein's post-translational modification (PTM) represents a major dynamic regulation of protein functions after the translation of polypeptide chains from mRNA molecule. Compared with the costly and labor intensive wet lab characterization of PTMs, the computer-based detection of PTM residues has been a major complementary technique in recent years. Previous studies demonstrated that the PTM-flanking positions convey different contributions to the computational detection of PTM residue, but did not directly translate this observation into the in silico PTM prediction. We propose a weight vector to represent the variant contributions of the PTM flanking positions, and use an evolutionary algorithm to optimize the vector. Even a simple nearest neighbor algorithm with the incorporated optimal weight vector outperforms the currently available algorithms. The algorithm is implemented as an easy-to-use computer program, jEcho version 1.0. The implementation language, Java, makes jEcho platform-independent and visually interactive. The predicted results may be directly exported as publication-quality images or text files. jEcho may be downloaded from http://www.healthinformaticslab.org/supp/ .
authors: Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, 518055, China.
authors: Miaomiao
authors: M
authors: Zhao
authors: Zhao
authors: Z
authors: Zhang
authors: Guoqin
authors: G
authors: Mai
authors: Youxi
authors: Y
authors: Luo
authors: Fengfeng
authors: F
authors: Zhou