Table 2.
Comparison of URPD with Primer3Plus, UniPrime2, and PDA
| Features | Software | URPD | Primer3Plus | UniPrime2 | PDA |
|---|---|---|---|---|---|
| Type |
web-based |
web-based |
web-based |
web-based |
|
| Availability |
http://bio.kuas.edu.tw/urpd/ |
http://www.bioinformatics.nl/primer3plus/ |
http://uniprime.batlab.eu/ |
http://dbb.nhri.org.tw/primer/ |
|
| Primer design method |
Memetic Algorithm (MA) & Genetic Algorithm (GA) |
Primer3-based |
Primer3-based |
✘ |
|
| User Interface |
intuitive user interface |
intuitive user interface, but complicated parameter settings |
intuitive user interface |
brief user interface |
|
| Sequence import |
single sequence or multiple sequences (high throughput) |
single sequence |
single sequence |
single sequence or multiple sequences (high throughput) |
|
| Accession No. input |
✓ |
✘ |
✘ |
✘ |
|
| UCSC In-silico PCR |
✓ |
✘ |
✘ |
✘ |
|
| NCBI blast check |
built-in |
hyperlink |
built-in |
✘ |
|
| Template annealing check |
✓ |
✘ |
✘ |
✘ |
|
| Pipeline leader |
✓ |
✘ |
✓ |
✓ |
|
| Ranking mechanism |
✓ |
✘ |
✘ |
✓ |
|
| Result file export |
text file |
text file |
e-mail |
MS-Excel |
|
| Visual PCR (gel electrophoresis) | ✓ | ✘ | ✘ | ✘ | |
Note: Symbol ✓ indicates that this function is included; symbol ✘ indicates that this function is not available.