The Musite open-source framework for phosphorylation-site prediction

BACKGROUND: With the rapid accumulation of phosphoproteomics data, phosphorylation-site prediction is becoming an increasingly active research area. More than a dozen phosphorylation-site prediction tools have been released in the past decade. However, there is currently no open-source framework specifically designed for phosphorylation-site prediction except Musite. RESULTS: Here we present the Musite open-source framework for building applications to perform machine learning based phosphorylation-site prediction. Musite was implemented with six modules loosely coupled with each other. With its well-designed Java application programming interface (API), Musite can be easily extended to integrate various sources of biological evidence for phosphorylation-site prediction. CONCLUSIONS: Released under the GNU GPL open source license, Musite provides an open and extensible framework for phosphorylation-site prediction. The software with its source code is available at http://musite.sourceforge.net.