Algorithm for designing conserved probes. Schematic illustration of the conserved sequence design method. (A) The similarity sequence segments (I1ito I5i) of a given virus v
are aligned with the sequence segments of the other five viruses within the same viral genus by the BLASTN program to find the regions with high similarity hits. (B) Graph of the numbers of similarity hits, S
, obtained by the procedure illustrated in panel A. The largest number of hits as illustrated is max(S
), which equals 4. The two regions with the highest similarity hits are marked by vertical dotted lines. (C) A case study of locating the conserved sequence segments in coronavirus genus. The genus contains the following 11 fully sequenced viral genomes: NC_002645, human coronavirus 229E; NC_001451, avian infectious bronchitis virus; NC_003436, porcine epidemic diarrhea virus; AF201929, murine hepatitis virus strain 2; AF208067, murine hepatitis virus strain ML-10; AF208066, murine hepatitis virus strain Penn 97-1; NC_001846, murine hepatitis virus strain A59; NC_003045, bovine coronavirus; AF220295, bovine coronavirus strain Quebec; NC_002306, transmissible gastroenteritis virus; and SARS-CoV, SARS coronavirus.