What'S The Best Way To Find Human Paralogs?

Question

[enricoferrero]

I have a list of human genes and I'd like to find all the paralogs in the human genome for each of them. What's the simplest way to do this? If reliable, I'd prefer using a database-based approach rather than a sequence similarity-based one.

My only idea so far has been to use Ensembl Biomart (via the Bioconductor biomaRt package) and use the Homologs --> Paralogs --> Human Paralog Ensembl Gene ID Attribute. Would that be a good approach? Anything else I could use instead?

Thanks!

[aravind ramesh]

I use http://dgd.genouest.org/ for human dupllicate genes. Hope this helps.

Answer 1

[fridhackery]

BLASTP. If your list is short do visual inspection of the top results. If your list is long, do enough visual inspection to choose an evalue or score threshold.