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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