Extract subset of Nr database

Question

[sbchua.1990]

I have downloaded and format (makeblastdb) the nr database from NCBI for my own local database (February 2017) . I want to extract subset from the nr database.

I have tried below method:

1. Download GIlist from NCBI
2. Use blastdb_aliastool to extract the subset.

Above method worked well for older database (2013) but show error "BLAST Database error: GI list specified but no ISAM file found for GI" for my recently download database. My understanding is NCBI no longer support GI.

I have also tried download target sequences as fasta file from NCBI directly as shown in http://www.ionsource.com/tutorial/db/tips_for_creating_species_specif.htm but download seem to be failed every time before complete.

Any other suggestion? I need to download nr database for txid5204[ORGN].

[Jake Warner]

Have you tried blastdbcmd?

http://nebc.nerc.ac.uk/bioinformatics/docs/blastdbcmd.html

Answer 1

[shenwei356]

try taxonkit, Extract all protein sequences of specific taxons from the NCBI nr database

[sbchua.1990]

Thanks for reply, Refer to the tutorial http://bioinf.shenwei.me/taxonkit/tutorial/ In step 2, 'prot.accession2taxid.gz' is just sample data for tutorial? If so, what is the equivalent of 'prot.accession2taxid.gz' for my data? I am a bit confused by that.

[shenwei356]

Of cause not! It's from NCBI: ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz

[sbchua.1990]

Thanks for your help. Good work on both 'taxonkit' and 'seqkit'. Both helped me a lot.

[shenwei356]

glad it helps, can you give this answer an upvote or and accept it?