Question: Where can I find human protein database to download for blastx?
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gravatar for grayapply2009
5.1 years ago by
grayapply2009180
United States
grayapply2009180 wrote:

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. 

blast human protein • 3.6k views
ADD COMMENTlink modified 5.1 years ago by 5heikki8.6k • written 5.1 years ago by grayapply2009180
1
gravatar for Jean-Karim Heriche
5.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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.

ADD COMMENTlink written 5.1 years ago by Jean-Karim Heriche21k
1
gravatar for Elisabeth Gasteiger
5.1 years ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

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.

 

ADD COMMENTlink written 5.1 years ago by Elisabeth Gasteiger1.7k
1
gravatar for 5heikki
5.1 years ago by
5heikki8.6k
Finland
5heikki8.6k wrote:

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

ADD COMMENTlink written 5.1 years ago by 5heikki8.6k

Thank you, guys. Let me have a try.

ADD REPLYlink written 5.1 years ago by grayapply2009180
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