Often the organism of interest only has a limited number of protein sequences available and the one for our target gene is not among them. One way to identify the gene sequence is through translated tblastn search against the nucleotide sequences from the target organism. We can use a known protein homolog from a well studied organism as query.
blastall -i hs_kal1 -d wgs -l guinea_pig.gi -p tblastn -o kal1_guinea_pig.out
The above command line searches the human kal1 protein (in hs_kal1 input file) against the preformatted wgs database from NCBI using tblastn. The search is limited to the guinea_pig entries specified by the guinea_pig.gi file generated through Entrez nucleotide search with wgs[prop] AND guinea pig[orgn]. Result is saved in kal1_guniea_pig.out. An example command line is given below.