Programs and links to online tools that will help you to evaluate PCR primers and the nucleotides in order ot allow for optimal PCR reactions and the necessary number of cycles. Numerous tools and links for oligo analysis, analysis of hairpin, self-dimer, heter-dimer, and other basic parameters.
| OligoAnalyzer from IDT - http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx/oligocalc.asp OligoAnalyzer from IDT, is a great tool that allows you to analyze short strands of dna, such as those for PCR primers. It allows you to analyze for future problems in primers, such as hairpins, and self-dimers, as well as many others. - [Read about OligoAnalyzer from IDT] |
| PCR Optimization Tool from Zbio.net - http://www.molbiol.ru/eng/scripts/01_14.html Great tool to optimize your PCR reactions for the best results. Has numerous parameters for input. - [Read about PCR Optimization Tool from Zbio.net] |
| PCR Box Titration Calculator - http://www.attotron.com/pub/pcrtitr.htm PCR Box Titration Calculator allows you to input numerous factors, including reagent concentrations, such as buffers, dNTPs, MgCl2, red sucrose and H2O to determine titration levels. - [Read about PCR Box Titration Calculator] |
| Oligo Calculator from Molecular Biology Protocols - http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=2110 Oligo Calculator from Molecular Biology Protocols, allowing you to find the best annealing and melting temperatures for your PCR primers. - [Read about Oligo Calculator from Molecular Biology Protocols] |
| OLIGOCALC - http://www.justbio.com/oligocalc/index.php OLIGOCALC allows you to determine your oligo size and length and relevant melting temperatures. - [Read about OLIGOCALC] |
| PCR Sequence Search Tool - http://genome.ucsc.edu/cgi-bin/hgPcr?org=Human&db=hg18&hgsid=99373706 UCSC In-Silico PCR allows a user to search a sequence database using a pair of PCR primers, using an indexing strategy for fast performance. - [Read about PCR Sequence Search Tool] |