Create a blastn species database

# merge all E. coli reference genomes into one ecoli.fasta file
cat genomes/ecoli_strains/*.fna > ecoli.fasta

makeblastdb -in ecoli.fasta -parse_seqids -dbtype nucl

  -parse_seqids is required to identify gene/contig IDs in mapping hits
  -dbtype   specifies the type of sequences: protein 'prot' or nucleotide 'nucl'


# Blast using species DB  (option:  -db)
blastn -query genes.fasta -db ecoli.fasta  -outfmt 6 -evalue 1e-30

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http://www.ncbi.nlm.nih.gov/books/NBK279688/