Question: ncbi database update
0
gravatar for anasofiamoreira94
14 months ago by
anasofiamoreira9470 wrote:

Good morning, I have some doubts concerning NCBI database. I'm using all database from NCBI, but now we only want to have some species, that are presented in the all database of NCBI. But now I'm not entirely sure on how to do this, because the goal is to eliminate some species in the result, and find out if with a shorten database we achieve precise results. Thank you for the help

blast news database • 748 views
ADD COMMENTlink modified 14 months ago by gb1.7k • written 14 months ago by anasofiamoreira9470

This is a Question and not a News post. I have changed it for you this time but please endeavour to use the correct post type in future.

ADD REPLYlink written 14 months ago by Joe16k

I'm sorry for the trouble and thanks for the help :)

ADD REPLYlink written 14 months ago by anasofiamoreira9470

You can create your own NCBI/BLAST databases. Simply download a collection of the genomes you wish to include in the database and use the tool makeblastdb.

ADD REPLYlink written 14 months ago by Joe16k

I've tried to do this command: blastdbcmd -db nt -taxids 3708 -out Brassica_napus.txt However i got this error: [blastdbcmd] Taxonomy list is not supported in v4 BLAST db.I really don't understand it.

ADD REPLYlink written 14 months ago by anasofiamoreira9470

Taxonomy list is not supported in v4 BLAST db

As I had noted below (with a link to new version), you need to download v5 Blast database indexes.

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax80k
2
gravatar for genomax
14 months ago by
genomax80k
United States
genomax80k wrote:

You can use the latest blast v.2.8.1 which has the option of restricting your searches to certain organisms. You may need to use the new blast database indexes (a different format) that is available from NCBI with this option.

-taxids <String>
   Restrict search of database to include only the specified taxonomy IDs
   (multiple IDs delimited by ',')
-negative_taxids <String>
   Restrict search of database to everything except the specified taxonomy IDs
   (multiple IDs delimited by ',')
-taxidlist <String>
   Restrict search of database to include only the specified taxonomy IDs
-negative_taxidlist <String>
   Restrict search of database to everything except the specified taxonomy IDs
ADD COMMENTlink modified 14 months ago • written 14 months ago by genomax80k
1
gravatar for gb
14 months ago by
gb1.7k
gb1.7k wrote:

As an addition to the accepted answer you can check the version by running:

blastdbcmd -db [yourdatabase] -info

If you used and want to use the script update_blastdb.pl

update_blastdb.pl nt_v5 --blastdb_version 5 --passive
ADD COMMENTlink written 14 months ago by gb1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 792 users visited in the last hour