Abstract Motivation: Pseudouridine (Ψ), catalyzed by pseudouridine synthase (PUS), is the most abundant RNA modification and has important cellular functions. Developing an algorithm to identify Ψ sites is an important work. And it is better if the algorithm could assign which PUS modifies the Ψ sites. Here, we developed PPUS (http://lyh.pkmu.cn/ppus/), the first web server to predict PUS-specific Ψ sites. PPUS employed support vector machine as the classifier and used nucleotides around Ψ sites as the features. Currently, PPUS could accurately predict new Ψ sites for PUS1, PUS4 and PUS7 in yeast and PUS4 in human. PPUS is well designed and friendly to user. Availability and Implementation: Our web server is available freely for non-commercial purposes at: http://lyh.pkmu.cn/ppus/ Contact: liyanhui@bjmu.edu.cn or cuiqinghua@hsc.pku.edu.cn