Hello all
I am looking for a script for locally annotation (NCBI-nr) of my data on a plant species which we have done de novo assembly on it . Does anyone have any script appropriate in this case? What do you think about this script?
blastx -query Flower-upregulated.fasta -db nr -out blastx.outfmt6 -evalue 1e-9 -num_threads 40 -max_target_seqs 1 -outfmt 6
Many Thanks
Have a look at Blast2GO. The pipeline will BLAST and give functional annotations to gene sequences or protein sequences that you give it. I'm fairly certain it has the ability to use a local BLAST database, as well.
See the supplementary of this paper: http://www.biomedcentral.com/1471-2229/14/329
We give scripts for running annotation tools and other scripts for integrating their results (if you choose to run more than a single pipeline)
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