How do I get description in BLAST?
Hi, all.
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
2) Add 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!
• 66 views
Read more here: Source link