Where can I find human protein database to download for blastx?

Question

[grayapply2009]

Where can I find human protein data base for local blastx? I have already blasted my transcriptome against the nr database. My adviser wants me to blast it against the human protein database and find out the genes named same way in both nr database and human database. I checked the ncbi ftp but couldn't find anything.

Answer 1

[Jean-Karim Heriche]

You can get all human proteins from EnsEMBL (using the API or BioMart). Alternatively, you can download human proteins from Uniprot's ftp site here.

Answer 2

[Elisabeth Gasteiger]

I suggest you have a look at these documents which explain how to retrieve and download all human proteins from the UniProt Knowledgebase:

http://www.uniprot.org/help/human_proteome

http://www.uniprot.org/help/retrieve_sets

One of the download formats is fasta (I recommend "fasta (canonical and isoforms)"), from which you should be able to generate a BLAST database.

Answer 3

[5heikki]

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/protein/protein.fa.gz

[grayapply2009]

Thank you, guys. Let me have a try.