Is it possible to remove the sequences of particular species from locally downloaded nr db of NCBI?
There is this option -negative_gilist in both blastn and blastp. You can use that to exclude a set of GI while doing your blast search against locally downloaded nr. To prepare a file containing GI of all the sequence from the concerned species, you can type the taxon id of your species as follows "txid559515" at NCBI nucleotide or protein search space
http://www.ncbi.nlm.nih.gov/nuccore/
http://www.ncbi.nlm.nih.gov/protein/
click on "sendto" and select "file" and select format as "GI list" and click on create file. It will download the GI of all the sequence available at NR that belong to the specific species of concern.
Then you can use this file in your local blast command as
blastn -query seq.fa -db nr -negative_gilist
(This is not a direct answer for how to exclude a species from nr database but the work around to deal with a situation when you are doing to blast search against NR and don't want hits from a particular species)
Hope that helps. :)
Depends. Did you download the pre-formatted binary BLAST db files, or the text FASTA files?
If you downloaded the FASTA files, you could parse them anyway you wish to since those are simple ASCII text files, and then create your own BLAST db files from those.
Thanks, I have downloaded the nr db. Is there any option/parameter to ignore any particular taxon for local blast (as we can do at NCBI online)
There is this option -negative_gilist in both blastn and blastp. You can use that to exclude a set of GI while doing your blast search against locally downloaded nr. To prepare a file containing GI of all the sequence from the concerned species, you can type the taxon id of your species as follows "txid559515" at NCBI nucleotide or protein search space
http://www.ncbi.nlm.nih.gov/nuccore/
http://www.ncbi.nlm.nih.gov/protein/
click on "sendto" and select "file" and select format as "GI list" and click on create file. It will download the GI of all the sequence available at NR that belong to the specific species of concern.
Then you can use this file in your local blast command as
blastn -query seq.fa -db nr -negative_gilist
(This is not a direct answer for how to exclude a species from nr database but the work around to deal with a situation when you are doing to blast search against NR and don't want hits from a particular species)
Hope that helps. :)
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