BLAST using both nucleotides and taxonomic local databases

Question

[Begonia_pavonina]

I try to BLAST a list of queries (queries.fasta) against a local mirrors of NCBI nucleotides database (nt) and taxonomic database (taxdb).

I run the following script (in R environment):

system2(
  blastn, 
  args = c(
      "-db nt",
      "-query queries.fasta",
      "-out results_r_script.csv",
      "-outfmt '6 delim=, 
      qseqid 
      sseqid 
      pident 
      length 
      sacc 
      slen 
      evalue 
      bitscore 
      score 
      staxids' ",
      "-evalue 1e-20",
      "-max_target_seqs 5"
)
)

I know that to use the taxonomic database, it is possible to use the taxids to find species and taxonomic ranks , with the library taxize for example. However, I was wondering if it is possible to get these information directly in a single blast, without using subsequent scripts to get taxonomic information?

I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST, but might be filled with a script I am not familiar with. If anyone know how, I would be interested in the answer!

[GenoMax]

I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST

If that information is missing from NCBI taxonomy database then it is likely that you won't find it using programs that depend on that database (not sure if taxize does).

shenwei356 has taxonkit (LINK) that you may find useful.But part of it depends on NCBI taxonomy.

Answer 1

[5heikki]

This has been discussed many times