I do not know how to identify pseudogenes of some gene family of rice, although I read many papers about it. I am very happy to see your good paper-Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation, but the Eukaryote Data databases do not include rice genome. I am not able to download PseudoPipe program from http://www.pseudogene.org as one paper mentioned. In fact, I can not find any program that lies at websever.Are you so kind to give me PseudoPipe program?
Unfortunately, we have not run our PseudoPipe program on the rice genome. The PseudoPipe software itself is rather complex and designed to run on a computing cluster. (It is computationally intensive) If you wish to try to install the software anyway, the source is located at http://www.pseudogene.org/DOWNLOADS/pipeline_codes/