Delete entry species from NCBi databse

Question

[anasofiamoreira94]

Good morning, Is it possible to exclude one species of the entire nt, NCBI database? Thanks for the help.

[gb]

From the help, think this can help you. You can see the full description if you put -help behind your command like blastn -help

-negative_gilist <String>
   Restrict search of database to everything except the specified GIs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
 -negative_seqidlist <String>
   Restrict search of database to everything except the specified SeqIDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
 -taxids <String>
   Restrict search of database to include only the specified taxonomy IDs
   (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc
 -negative_taxids <String>
   Restrict search of database to everything except the specified taxonomy IDs
   (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
   subject_loc

[lieven.sterck]

Hi, could you elaborate on this question?

What is the goal? do you mean in a local setting or remove from the official releases as well?

[anasofiamoreira94]

In my analysis, we perform the analysis using blast against all database, so the goal would be to delete in a local setting.

[Bastien Hervé]

I think you want to "exlude" species from blast process. Do you have a blast command line we can start with ?

[anasofiamoreira94]

I use this command line: 'blastn -task megablast -num_threads 6 -outfmt "6 std ssciname" -max_target_seqs 1 -db nt_v5 -query ' + clustfastareps + " -out "+blastfile' Thanks for the help

[lieven.sterck]

also, be careful with using -max_target_seqs 1 , it might in some cases not do (or result) in what you expect it to do. There are some threads here on Biostars about it.

EDIT: and outside Biostar as well as indicated by Bastien Hervé !

[Bastien Hervé]

https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-repartee-one.html

[anasofiamoreira94]

Thank you for the help

[lieven.sterck]

ok, that' s one thing already

anyway, we would need more info to be able to assist you, which DBs are you referring to? what kind of analysis?

[anasofiamoreira94]

I'm sorry, I'm using all nt.

Answer 1

[GenoMax]

You can use the following option to eliminate a specific species (find its taxid from Tax Browser):

-negative_taxids <String>
   Restrict search of database to everything except the specified taxonomy IDs
   (multiple IDs delimited by ',')