Pseudouridine (xcexa8), catalyzed by pseudouridine synthase (PUS), is the most abundant RNA modification and has important cellular functions. Developing an algorithm to identify xcexa8 sites is an important work. And it is better if the algorithm could assign which PUS modifies the xcexa8 sites. Here, we developed PPUS (http://lyh.pkmu.cn/ppus/), the first web server to predict PUS-specific xcexa8 sites. PPUS: employed support vector machine as the classifier and used nucleotides around xcexa8 sites as the features. Currently, PPUS: could accurately predict new xcexa8 sites for PUS1, PUS4 and PUS7 in yeast and PUS4 in human. PPUS: is well designed and friendly to user.