This search involves the translation of the input nucleotide query and the actual alignment is performed at the protein level. It is useful the identification of potential protein product(s) that might be encoded by a nucleotide query, especially when the query may still contain sequencing errors. Since the alignment is done at the protein level, it is more sensitive in identifying homologous sequences that may escape the direct nucleotide search. A sample command line is given below.
blastall -p blastx -i my_query -d nr -v 100 -b 100 -e 0.001 -o my_output
This command line searches nucleotide sequences in my_query against the protein database nr. The upper limit for returned descriptions and alignments is set to 100, the expect value cutoff is set to 0.001, and the output is saved to my_output.