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