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.

The viral sequence database is dominated by gene fragments We queried the EMBL viral database to determine the frequencies of coding sequences and full genomic sequences. The majority of viral sequences were <1 kb 1982 1984 1986 1988 1990 1992 1994 1996 1998 A commonly used method to reduce sequence complexity is generation of a non-redundant sequence set by clustering (33) . We grouped sequences at the 98% identity level and selected the longest sequences as unique representatives of each group. This method was used to assess the growth of sequence diversity between January 2000 and the current release of July 2007. The database grew 600% in the 7-year period; doubling every three years. Unique sequences decreased as a proportion of the database, from 42% to 27%; overall growth of unique sequences was 378% (Figure 1b) . The current database comprised 74 044 unique sequence representatives at the 98% similarity level. Thus, the growth in the number of sequences in the viral database has been rapid, while growth in diversity has been more modest.