[MUMmer-help] Using MUMMER to infer pseudogene intron loss?

[Anand K S R. <ak...@uc...>]

I have not yet used MUMMER for any of my analyses.
Therefore, I seek your help to decide whether MUMMER3.0 can be a suitable
tool for the following *objective*:

Using a 3rd party analysis pipeline, I have generated a set of predicted
pseudogenes - both processed and non-processed.

At the moment, I cannot distinguish these 2 cases. But, my goal is to
identify processed pseudogenes. One way to do this is to compare the number
of introns in pseudogene to that in sister gene.

*Work so far*

I have mapped each predicted pseduogene to its best sister gene. The
pseudogene was identified in the 1st place, using the sister protein as a
tBLASTn query.

*The Objective: Can MUMMER do this?*

I want to know whether MUMMER can align the predicted pseudogene to its
sister gene. Either directly at the DNA sequence level, or via intermediate
steps involving cDNA / protein from the sister gene. Will such an approach
help 'count' the introns in sister gene Vs pseudogene, and thereby help
infer whether a predicted locus may have been generated as a retrogene or
not?

*Info available*

I have the following information at my disposal:
1. Coords and DNA sequence of pseudogene prediction
2. Sister gene DNA sequence
3. Sister gene full-length cDNA sequence
4. Sister gene full-length protein sequence
5. Sister gene protein sub-sequence that matches the pseudogene coords

Thank you all, in advance!