Q:
The pseudogene databases, including Pseudofam and PseudoPipe, have been extremely helpful for a project I am working on, and I was wondering if you knew how it would be possible to compare the DNA sequence of a human gene with all the pseudogenes on the PseudoPipe resources. I am looking to identify pseudogenes that may be related to the genes I am working with. I was hoping there was a way to devise this information by BLAST comparing the DNA sequence a specific gene with the sequences from all the pseudogenes in the genome, similar to NCBI BLAST or UniProt BLAST feature.

Any help or insight would be appreciated.

A:
If you have many genes to query, may be you can use BLAST+ (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) to build your own tool. You can then download the sequences of all pseudogenes and make a BLAST database (https://www.ncbi.nlm.nih.gov/books/NBK279688/ ) from which you can query.