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 | |||||
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 | MS-Excel | ||
Visual PCR (gel electrophoresis) | ✓ | ✘ | ✘ | ✘ | |