title: jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.
abstract: Protein's posttranslational 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 laboratory 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.affiliation: Shenzhen Institutes of Advanced Technology, Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, 518055, China.
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Zhao
authors.forename: Zhao
authors.initials: Z
authors.lastname: Zhang
authors.forename: Guoqin
authors.initials: G
authors.lastname: Mai
authors.forename: Youxi
authors.initials: Y
authors.lastname: Luo
authors.forename: Fengfeng
authors.initials: F
authors.lastname: Zhou
mesh_terms: D020816:Amino Acid Motifs; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D012985:Software Design; D060388:Support Vector Machine