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Delete entry species from NCBi databse

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

ncbi databse
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written by anasofiamoreira94 anasofiamoreira94

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?

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written by lieven.sterck lieven.sterck

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

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written by anasofiamoreira94 anasofiamoreira94

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?

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written by lieven.sterck lieven.sterck

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

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written by Bastien Hervé Bastien Hervé

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

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written by anasofiamoreira94 anasofiamoreira94

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 !

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written by lieven.sterck lieven.sterck

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
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written by gb gb

1 answer

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 ',')
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written by GenoMax GenoMax

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