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- Title
jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.
- Authors
Zhao, Miaomiao; Zhang, Zhao; Mai, Guoqin; Luo, Youxi; Zhou, Fengfeng
- 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 .
- Subjects
POST-translational modification; PROTEINS; POLYPEPTIDES; MESSENGER RNA; COMPUTER software; COMPUTER algorithms
- Publication
Interdisciplinary Sciences: Computational Life Sciences, 2015, Vol 7, Issue 2, p194
- ISSN
1913-2751
- Publication type
Article
- DOI
10.1007/s12539-015-0260-2