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.

Whereas probe design in motif-based arrays can exploit partial genome sequences, probes in tiling arrays are based on full length genome sequences. Complete Reference Sequence genomes represent 1% of EMBL sequence entries. Although at least one full length genome sequence is described for all viral genera, only 49% (1701 of 3441) of viral species have a fully sequenced representative genome. The impact of differences in the motif and tilingbased strategies for probe design is reflected in differences in coverage. For the tiling-based probe-set, 40 of 44 families with <80% sequence coverage included species lacking representative genomes. Coverage with motifbased probe-sets for these same species was !93%.