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Table 1 Comparison of selected features among different primer design tools

From: Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

 

Primer-BLAST

QuantPrime

PRIMEGENS

General

   

  Scope of primer design task

General purpose

Real time PCR only

General purpose

  Alignment algorithm for specificity checking

Local and global

Local only

Local only

Specificity checking options

   

  Specify a range for the number of nucleotide mismatches   required between primer and unintended targets

Yes

No

No

  Define a custom region at 3’ end where certain number of nucleotide   mismatches must exist between primer and unintended target

Yes

No

No

  Number of organisms covered by mRNA and genome databases

7546

333

18

Exon/intron requirement settings

   

  Place primers across exon/exon junction

Yes

Yes

No

  Place primer pairs that span an intron

Yes

No

No

  Set custom nucleotide match on either side of exon/exon junction

Yes

No

No

Other primer design options

   

  Allow custom PCR template sequence in FASTA format

Yes

No

Yes

  Avoid SNP in primers

Yes

Yes

No

  Allow specificity checking for pre-existing primers

Yes

No

No

Result presentation

   

  Graphic overview of primers found

Yes

No

No

  Detailed nucleotide alignments between primers and targets

Yes

No

No