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Table 2 Main features of similar web-based primer design tools

From: TipMT: Identification of PCR-based taxon-specific markers

Tool Sequence input Search for Target sequences Specificity check method Output Multiplex check
BatchPrimer3 multiple sequences (up to 500) yes
(SSR, SNP)
none primers information no
jPCR multiple sequences yes
(SSR only)
alignment primers information yes
MPprimer multiple sequences no thermodynamic
(limited and pre-defined list of sequences)
primers information and virtual gel yes
TipMT multiple sequences from multiple taxa yes
(SSR, orthologs, singletons)
alignment and thermodynamic primers information and virtual gel yes
  1. TipMT offers a combination of features that are not present in any other web application: multiple sequences as input, identifies target regions automatically in a single run, tests the specificity with two approaches and generates a virtual electrophoresis gel as output