pseudogenes and their parent gene common regions

Question

[asalimih]

Hi,
I have a list of gene names and their corresponding pseudogenes. I want to figure out which regions of a pseudogene and its parent gene are common. I think one way would be first extracting their sequence then align them to each other with some tool like bwa.
Is there a way, tool or database so I can do this task more easily. preferably offline method.

also I should mention that the final aim of this work is to find if a predicted variant in a gene is in a position which is common between the gene and one of it's pseudogenes. any help would be greatly appreciated.

[GenoMax]

their sequence then align them to each other with some tool like bwa.

You will need to use a pair-wise sequence alignment tool and not an aligner like bwa.

[asalimih]

you are right. what do you suggest for this purpose? blast, splign ...

[ACTG]

Hi, I came across your post about identifying common regions between pseudogenes and their parent genes. I’m currently facing the same challenge and would love to know if you were able to find a solution. If so, could you please share the method or tools you used? Any guidance or suggestions would be immensely helpful!

Thanks in advance!

Answer 1

[Anand Rao]

Assuming you are working with the human genome, or even otherwise, have you looked into PseudoPipe or PseudogenePipeline?

Since you already have the list of genes and pseudogenes, this might be overkill though. In which case, you may want to ping Shin-Han Shiu - the PI for Pseudogene Pipeline research group for his advice on which specific steps / scripts / wrappers would be sufficient to align your genes to your pseudogenes to identify your pairwise mappings.

Since the time I've used PseudogenePipeline, it's undergone quite a few changes, and I unfortunately do not have the spare time right now to delve into it again. Good luck!

[asalimih]

Thanks. yes it is human genome.