From: Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
 | Primer-BLAST | QuantPrime | PRIMEGENS |
---|---|---|---|
General | Â | Â | Â |
  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 | Â | Â | Â |
  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 | Â | Â | Â |
  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 | Â | Â | Â |
  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 | Â | Â | Â |
  Graphic overview of primers found | Yes | No | No |
  Detailed nucleotide alignments between primers and targets | Yes | No | No |