Comprehensive viral oligonucleotide probe design using conserved protein regions

Jabado, Omar J.; Liu, Yang; Conlan, Sean; Quan, P. Lan; Hegyi, Hédi; Lussier, Yves; Briese, Thomas; Palacios, Gustavo; Lipkin, W. I.

All four subtypes were subjected to the same three step design method: identification of conserved regions, extraction of nucleotide probe sequences, and minimization of covering probes. By allowing a limited number of mismatches to cognate templates, the number of probes required can be reduced. The mismatch threshold was determined based on experiments with West Nile virus (strain New York 1999, AF202541) that indicated high, homogenous fluorescence signal was observed if probes had five or fewer mismatches to the viral template ( Figure 2 ). The probe minimization technique serves to lower microarray printing costs and simplify analysis while maintaining sequence coverage. A flowchart of the design method is depicted in Figure 3 .