List of Known Pseudogenes or Known Protein-Coding Genes named with ENSG tag

[ddmoore1028]

Hi All,

I am looking for a list of known pseudogenes labeled with the ENSG naming convention to match to a set of data that I have comparing different aligners. I want to separate pseudogenes from protein coding genes. So, alternatively, I could use a list of protein coding genes named by the same convention. Does anyone know where/how I can find such a list? This is to keep from manually researching every gene in my data to see if it is a pseudogene.

Thanks,

Dalton

[GenoMax]

You can use BioMart from Ensembl (http://www.ensembl.org/index.html).

Once you click on "BioMart" in the top menu options:

Select an Ensembl data set (e.g. Ensembl genes 72)
Select the genome you want (e.g. Human GRCh 37)
Use the "filters" --> Select "Gene" --> "Gene Type" --> "Pseudogenes"/"Protein_Coding"
Hit the "count" button at the top left (15524 / 63253 pseudogenes for Human at the moment).

You can then click on "Attributes" and select the appropriate attributes to download.

Look for YouTube tutorials for BioMart if you need additional help.