Dear all,

I need to perform a large BLAST search and I am using blastn in remote from the terminal. However, this takes way too long to give an answer and I have been thinking of creating a local database to speed the analysis. How can I download the all nr/nt repository? I see there is one [here][1] for the RefSeq. Would be this good? would it be already indexed or shall I create the index with makeblastdb?

Thank you


  [1]: https://www.ncbi.nlm.nih.gov/refseq/
You can use

    wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz

    wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz

These are fasta files, they are not indexed. You should use the `makeblastdb` command to index that. 

You might also want to browse ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA and check what other databases are available. 
