[Genome] Processed pseudogenes

[Rebecca Robilotto]

Hello,

I am working on a project that involves looking at the syntenic regions
between C. elegans and C. Briggsae. In the chain and net files I found that
it creates it own subset of syntenic regions. We have a set of pseudogenes
that I want to compare with the syntenic regions to see if there is any
relationship. I was reading the PNAS paper Evolution's cauldron:
Duplication, deletion, and rearrangement in the mouse and human genomes and
it mentioned that the NETFILTER program creates the syntenic subset and it
includes the pseudogenes that arise from tandem duplication, but it
eliminates the processed pseudogenes information. This paper discusses mouse
and human, but I was wondering it has the same result with C. elegans and C.
Briggsae. I would like to know about all the possible pseudogenes. Is there
a way that I could get all the pseudogene information in the chain and net
file and not just the duplicated ones?

Thank you,
Rebecca Robilotto