Question: getting sscinames in viral blastx query
0
gravatar for irritable_phd_syndrom
3.4 years ago by
irritable_phd_syndrom60 wrote:

I am running a local blast instance on my computer and I am trying to extract the sscinames from the database.  I downloaded the viral database from ftp.ncbi.nlm.nih.gov/refseq/release/viral and created the blast database (with taxID) via : 

 grep -i "Viral\|virus" /reference/blast_database/refseq/RefSeq-release74.catalog &> viral_taxid.txt

awk 'BEGIN{FS= "\t"}{print $3" " $1}' viral_taxid.txt &> viral_taxid_map.txt

cat viral.2.protein.faa viral.1.protein.faa &> combined.protein.faa

makeblastdb -parse_seqids -in combined.protein.faa -out combined.protein -dbtype prot -taxid_map viral_taxid_map.txt

 

When I blast against my database, e.g.

blastx -num_threads 1 -outfmt '6 qseqid evalue bitscore staxids sgi sacc sscinames stitle' -db combined.protein -query data.fa

it does not return the sscinames.  Is there a way to incorporate this into my blast database?

 

Thanks.

 

blast refseq • 1.0k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by irritable_phd_syndrom60
2
gravatar for irritable_phd_syndrom
3.4 years ago by
irritable_phd_syndrom60 wrote:

SOLUTION : I "export BLASTDB="/path/to/taxdb" which is the directory where taxdb.btd and taxdb.bti are installed.

ADD COMMENTlink written 3.4 years ago by irritable_phd_syndrom60
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