I am using blast+ tools on the command line with local databases. I would like to do a blast against nr limiting the search to a given taxon, just as one can do in the blast web. Is that possible? Thanks in advance for your any insight.
This is done by creating a list of GIs that belong to the the taxon. Search the manual for limiting to organism.
Solution:
1. Get gi list eg (all gis from Homo Sapiens proteins)
1.1. In http://www.ncbi.nlm.nih.gov/ search in proteins with the following string: Homo Sapiens [Organism]
1.2. Under Send to, choose File, Format Gi list, create file. That will download al gi into a file named sequence.gi.txt
2. Do blast
blastp -query seq.fasta -gilist sequences.gi.txt -db nr
Alternative method using a remote search of NCBI databases:
blastp -query seq.fasta -db nr -remote -entrez_query "Homo sapiens [Organism]"
Pros: Don't have to download individual gi lists
Cons: Requires internet connection, may be slower as it uses NCBI servers to complete the search
This is coming late (but this answer did not exist at the time the question was asked). In 2018, NCBI did update the blast database format from version 4 to 5 (https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf). Version 5 is taxon-aware and if you use a blast executable >= 2.8 you should be able to limit a local blast search to a specific species (or a list of species). I have tried it out and it works, but for some reason feels very slow as if searching the whole database and then merely pruning the results. I cannot imagine that this was the way it was implemented, but maybe the new executables are not yet finetuned for performance.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics