Advances in Bioinformatics / 2014 / Article / Tab 3

Research Article

Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

Table 3

Number of nontarget amplicons predicted in a multiplex reaction of tiled primers for 3 kb amplicons. In a multiplex of the 3 kb-amplicon tiled primers for a given organism, of the possible reactions producing products, only a small number of primer combinations are predicted to amplify regions in nontarget organisms. Counts show the number of unique primer combinations in a multiplex that yield products for any sequence in the NCBI nt nucleotide database. The numerator is for any nontarget organism in nt and the denominator is for any target or nontarget organism in nt, that is, nonspecific/total of the possible primer combinations in the multiplex predicted to yield product when compared against nt. Vastly more amplicons are produced from target organisms, indicating any contaminating nontarget species should be a small minority of amplified product.

OrganismNontarget amplicons/total ampliconsNontarget amplicon source organism

CCHF_S0/160
CCHF_M0/1934
CCHF_L0/3753
RVF_S0/137
RVF_M0/356
RVF_L0/753
Ebola1/2657Zea mays clone BAC ZMMBBb0342E21
Marburg0/1511
Hendra0/206
Nipah0/286
Junin_L0/69
Machupo_L0/153
Junin_S0/84
Machupo_S0/32
JEV7/9515Rocio 
West Nile
NW_Arena_S56/1543Ippy 
Lassa 
Luna 
Lymphocytic choriomeningitis 
Mobala 
Mopeia
NW_Arena_L0/819
OW_Arena_S73/2509Allpahuayo 
Amapari 
Bear canyon 
Chapare 
Cupixi  
Dandenong 
Flexal 
Guanarito 
Junin 
Latino
Lujo
Machupo
Methylococcus capsulatus str. Bath
Parana
Pirital
Sabia
Tamiami
Whitewater Arroyo
OW_Arena_L1/1826Dandenong
TBEV0/4925