This search is generally reserved as a last resort when all the other searches, blastn, blastp, blastx, and tblastn mentioned above, fail to return any useful information. Due to the computational intensity, it takes much more time to complete. In addition, tblastx searches tend to have a much higher noise to signal ratio. This makes the interpretation of result difficult and time consuming. It should be used with caution. An example command line is given below.
blastall -i e_coli_mutL.ORF -d wgs -l Ferroplasma_gi -p tblastx -o Ferroplasma_mutL.out
The above command line attempts to find the mutL counterpart in Ferroplasma through tblastx search. The search is limited to Ferroplasma portion through the input Ferroplasma_gi file, generated using Entrez nucleotide search with wgs[prop] AND Ferroplasma[orgn].