Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: blastn linux command specify database
0
gravatar for chrisclarkson100
3.6 years ago by
chrisclarkson100 • 80
European Union
chrisclarkson100 • 80 wrote:

I'm trying to run a local linux blast search and I know the general formatof the command: blastx -query seqs.fasta -db nr -out output.blast.txt. However I don't know the short names for all the databases I want to search e.g. "ena_fun". How can I find these inputs out?

Thanks
blast • 4.5k views
ADD COMMENT • link •
modified 3.6 years ago by Philipp Bayer ♦ 6.3k • written 3.6 years ago by chrisclarkson100 • 80
1
gravatar for Philipp Bayer
3.6 years ago by
Philipp Bayer ♦ 6.3k
Australia/Perth/UWA
Philipp Bayer ♦ 6.3k wrote:

You have two avenues to choose:

1. You run BLAST locally, but use a remote database using the flag -remote. In that case, you can choose a database from this list

(link via List of NCBI database names for standalone BLAST remote search )

2. You run BLAST locally with a local database. In that case, you can use any protein/nucleotide file. You need to format it using

    makeblastdb -dbtype prot/nucl (depends on whether you have proteins or nucleotides) -in your_filename

Then you can use the name of the file you used for makeblastdb as argument for the -db flag in blastx.
ADD COMMENT • link written 3.6 years ago by Philipp Bayer ♦ 6.3k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 725 users visited in the last hour