Figure 3

In silico validation of the conserved sequence design method. All of the fully sequenced viral genomes (except that of SARS-CoV) in the coronavirus genus were used to determine the conserved sequences. The design method was validated by testing if the computed conserved sequences could successfully detect the novel SARS-CoV. (A) The redundant conserved segments as computed by steps 1 to 4 of the probe design algorithm were reduced to five nonredundant sequence groups by the BLASTN sequence alignment in step 5 of the probe design algorithm. The longest sequence (underlined sequence) in each group was used to represent the group. (B) BLASTN results for the comparison of the group 1 conserved sequence with the SARS-CoV genome. The BLASTN alignment outputs are shown in the figure. The sequence alignment with the SARS-CoV genome shows that the group 1 conserved sequence is located between nucleotides 15732 and 15829 of the SARS-CoV genome. (C) Larger-scale cross-validation of 14 viral genera consisting of 333 nonredundant sets of viral genomes.