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Table 2 Comparison of URPD with Primer3Plus, UniPrime2, and PDA

From: URPD: a specific product primer design tool

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)
  1. Note: Symbol indicates that this function is included; symbol ✘ indicates that this function is not available.