Musite Yet another bioinformatics tool to help you with your work.
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calculator calculate protein bioinformatics visual platform bioinformatics bioinformatics library bioinformatics tool bioinformatics GUI bioinformatics package bioinformatics workflow P2P bioinformatics service bioinformatics service bioinformatics problem UCSC genome bioinformatics handle bioinformatics data bioinformatics toolkit bioinformatics data warehouse

Musite Description

Musite is an easy to use, Java based application designed to offer a bioinformatics tool for predicting both general and kinase-specific protein phosphorylation sites. Main features: To address the various limitations of current tools when applying to proteomes and to better utilize the large magnitude of experimentally verified phosphorylation sites, we developed a unique standalone application system Musite, specifically designed for large-scale prediction of both general and kinase-specific phosphorylation sites. Musite utilized local sequence similarity patterns (KNN scores) and generic features (disorder scores and amino acid frequencies) of phosphorylation sites, and employed a comprehensive machine learning approach to make predictions. We confirmed the previous finding that phosphorylation sites are preferentially located in disordered regions on phosphoproteomics data in six organisms. Musite is the first tool that provides utility for training a phosphorylation-site prediction model from users' own data and supports continuous adjustment of stringency levels. Musite provides a user-friendly graphic user interface, which makes it easy for biologists to perform predictions in an automated fashion. Applications of Musite on six proteomes yielded tens of thousands of putative phosphorylation sites with high stringency. These predictions provide useful hypotheses for experimental validations. Cross-validation tests show that Musite significantly outperforms existing tools for predicting general phosphorylation sites and is at least comparable to those for predicting kinase-specific phosphorylation sites. Moreover, as an open-source software, Musite can be also served as an open platform for building machine learning application for phosphorylation-site prediction.

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