Can you provided me with the data you used for the paper "A computational approach for identifying pseudogenes in the ENCODE region"?
The paper should point to you all the input data, which can be downloaded from the Ensembl website. If you want to know more details about the computational process, you might find them in the following paper too.
http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1437
In fact, it might be easy for you to re-produce the computational pipeline described in the above paper.
