Entering edit mode
6.9 years ago
4galaxy77
2.8k
If I am locally running a blastx against the nr database I downloaded, is it possible to specifiy only hits to mammals (taxid = 40674), for example? My blast run is taking quite a long time and I am hoping that it might speed it up if I filter for the taxonomy I am interested in. Or is this something which needs to be done when I am formatting the database?
Sorry if this question is a bit obvious, but I struggle with the wording on the NCBI website. Thanks.
Vertebrate Subset Nr Database? Build My Own?
I don't think it is possible to limit BLAST database output to a specific taxonomy ID. Maybe you can look into DIAMOND instead of running BLASTX as it's much faster than BLASTX.
If you use outfmt 6 or 7 you could try including the staxid column and filter by that.