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.

There is an increasing appreciation for the power of microarray technology in clinical microbiology, public health and environmental surveillance. Viral microarray probe design poses unique challenges due to the rapid increase in sequence data and the high propensity for sequence divergence within viral taxa. To ensure coverage of the newest isolates it is essential to consider partial as well as complete genomic sequences in probe design. Probe design based on multiple alignments or pairwise comparisons of nucleic acids for all known sequences is computationally intensive and scales poorly with database size. Protein sequence comparisons are rapid and incorporate rich evolutionary models, but require a cumbersome mapping step to extract underlying nucleic acid sequence. We have described a method that capitalizes on the Pfam protein alignment database and a motif finding algorithm to automate the extraction of nucleic acid sequence for probes from conserved protein regions. The protein motif-centric method has several advantages: (i) the majority of viral nucleic acid sequences encode proteins; thus, using this information leverages knowledge about function; (ii) protein sequence comparison and the resulting probesets are independent of viral taxonomy; this may enable incorporation of misclassified sequences; (iii) the Pfam is a well established and highly annotated database that will provide a basis for future design efforts; and (iv) probes designed in conserved regions may be able to detect novel viruses.