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.