Advances in Bioinformatics / 2014 / Article / Tab 1

Research Article

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

Table 1

Summary of average lengths, number of sequences, and percentage of conserved bases in a multiple sequence alignment (with MUSCLE [5]), and number of tiled primers required for the short and long amplicon settings.

OrganismNumber of sequencesAvg. LengthConsensus (%)Number of primers for ~3,000 bp ampliconsNumber of primers for ~10,000 bp amplicons

CCHF_S5616683966
CCHF_M495314244616
CCHF_L3112113466927
RVF_S8916845322
RVF_M6938857846
RVF_L6264048364
Ebola2218659511635
Marburg311911570348
Hendra101823497124
Nipah91824791186
Junin_L1271149662
Machupo_L5714188102
Junin_S2634108044
Machupo_S1334327644
JEV1441096856266
NW_Arena_S1003396186442
NW_Arena_L427107188319
OW_Arena_S543547811632
OW_Arena_L4571992111035
TBEV6710840365610

Abbreviations: CCHF = Crimean-Congo hemorrhagic fever, RVF = Rift Valley fever, JEV = Japanese encephalitis virus, NW_Arena = New World Arenavirus, OW_Arena = Old World Arenavirus, TBEV = tick-borne encephalitis virus, _L = L segment, _S = S segment.

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