I'm trying to get a description to the gene list using BLAST. I created the original database with the following command and did BLAST, but my output shows a lot of N/A.
$ makeblastdb \ -in caenorhabditis_elegans.PRJNA13758.WBPS16.protein.fa \ -out elegansdb \ -dbtype prot \ -parse_seqids $ blastx \ -query genes.fasta \ -db /home/nkarim/blast/db/elegansdb \ -outfmt "6 qseqid salltitles sseqid sscinames scomnames staxid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore" \ -evalue 1e-3 \ -out results
I have tried all the commonly suggested solutions.
1) Download taxdb.tar.gz in the same directory as the database, and unzip it.
$ update_blastdb.pl taxdb $ tar -xvf taxdb.tar.gz
export BLASTDB=$BLASTDB:/home/nkarim/blast/db to ~/.bashrc and reload.
Are there any other problems for me? I'm facing this problem for few days but can't solve it.
I really appreciate for your help in advance!
with exactly do you mean with " shows a lot of N/A " ? That you don't get any hit or that there is no usable functional description for the hits reported?
I share some of results. It means partial N/A is displayed.
Can you show us what the fasta headers of the input database fasta looked like?