Table 2.
Summary of results of primer set prediction for several diverse RNA virus species for primers of length 10 or 17–18 nt, the longest stretch of bases conserved among the targets in a multiple sequence alignment, illustrating the difficulty of selecting conserved primers, and the time required to perform the primer set selections
| Virus species | Number of sequences | Number of 10-mers | Number of 17–18-mer primers in set | Longest conserved region from MSA (nt) | Processing time on 1 cpu of an AMD Opteron to calculate 10-mer primers (hours) | Processing time on 1 cpu of an AMD Opteron to calculate 17–18-mer primers (hours) |
|---|---|---|---|---|---|---|
| NA segment of Influenza A* | 6375 | 52 | 120 | 5 | 5.7 | 28.9 |
| HA segment of Influenza A* | 5440 | 73 | 153 | 1 | 6 | 29.5 |
| HIV-1 | 1175 | 6 | 16 | 0 | 1.6 | 9.1 |
| FMDV | 187 | 4 | 6 | 9 | 0.18 | 0.7 |
| Norwalk | 41 | 7 | 20 | 6 | 0.1 | 0.5 |
*For Influenza A HA and NA segments, all complete sequences, including lab strains, from all hosts, countries and serotypes were downloaded from the NCBI Influenza Virus Resource database (http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/multiple.cgi) on 18 January 2008.
Primer sequences are provided as Supplementary Data.