Question: Getting scientific name (ssciname) in Blastn output
1
gravatar for brianna.flynn
27 days ago by
brianna.flynn10 wrote:

Hey all,

I would like to get the scientific names of each of my blast hits from blastn run locally. I have downloaded the taxdb.tar.gz taxonomy database from NCBI and have set the $BLASTDB variable to the directory with my blast database and query contigs. In my tabbed output, all I get is an 'N/A' in the spaces where the scientific names should be present. I was wondering if I am missing an important step in the taxonomy database installation?

$ export BLASTDB=$BLASTDB:/path/to/myblastdb
$ blastn -db all_viruses.fasta -query my_contigs.fasta -max_target_seqs 200 -evalue 0.001 -outfmt "6 qseqid sseqid sscinames qcovs pident evalue bitscore length" -out my_blast_results

Thank you in advance, Brie

blast alignment • 148 views
ADD COMMENTlink modified 21 days ago • written 27 days ago by brianna.flynn10
0
gravatar for Amar
26 days ago by
Amar620
Amar620 wrote:

What blast version are you using? Try ssciname. Not the singular form.

I think you have an older version. Always good practice to post what version num you're using so we can trouble shoot. Also try staxids it's not exactly what you're after but might help you get there.

ADD COMMENTlink written 26 days ago by Amar620
0
gravatar for brianna.flynn
21 days ago by
brianna.flynn10 wrote:

Hi Amar! I finally got it to work for me by downloading the accession2taxid file from the NCBI FTP site, and then creating a new blast database with the taxids using the option -taxid_map following this post: Scientific Names In Blast Output And Databases

ADD COMMENTlink written 21 days ago by brianna.flynn10
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