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BLASTx

for mapping a nucleotide sequence against a protein database
nucleotide sequences are translated automatically by BLAST

blastx -query DNA_gene_sequences.ffn -subject protein_sequences.faa  -outfmt 6 -evalue 1e-50


BLASTx options
http://www.ncbi.nlm.nih.gov/books/NBK279675/table/appendices.T.blastx_application_options/