Installation of PPFinder

Question

[subashini.fbtpb106]

Hi,

I am working on mining pseudogenes from Clarias sp. It is in the form of assembled scaffolds. I have masked the repeats using Repeat masker (Hard masking). I have predicted the parent protein data set using Augustus software. I need to know whether I need to mask pseudogenes from this parent protein set before going for tBLASTn. I am not able to download PPFinder which masks pseudogenes and iterate the gene prediction. Can anyone please the share the download link which is working?

[ATpoint]

Is this software from 2006 really still the go-to solution for your problem? You apparently already face problems before even starting with it. I personally would try to scan recent papers on the matter and see whether they use something more recent.

[subashini.fbtpb106]

Can you suggest me any software that does gene prediction by masking pseudogenes?

Answer 1

[GenoMax]

Since the software is still listed on the Brent lab website your best bet would be to email the investigator and ask that they fix the link for the software download. The email address can be found at the bottom of the page linked.