Hi,
I have predicted pseudogenes in Populus trichocarpa using Shiu's pipeline and want to know the parent genes of these predicted pseudogenes. I performed blastn with predicted pseudogene sequences as query input and "the concatenated exonic DNA sequence per locus/transcript (coding genes only), from start codon to stop codon" as the database to be compared to.
Because I specifically predicted for duplicated pseudogenes, I expect that for most pseudogenes I should be able to find a parent gene, but in my output the majority of pseudogenes didn't have any predicted parent genes. Because of this surprisign result, I tried the same for Arabidopsis thaliana, but got similarly bad(?) results.
My question therefore is if someone has experience in finding the parent genes of pseudogenes to tell me if the results I produced are to be expected or not. Additionally I'd like to ask if anyone has better ways of predicting pseudogene parent genes.
