ncbi database update

Question

[anasofiamoreira94]

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

[Joe]

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.

[anasofiamoreira94]

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

[Joe]

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.

[anasofiamoreira94]

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.

[GenoMax]

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.

Answer 1

[GenoMax]

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

Answer 2

[gb]

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