Software Links

Obtain Target Sequence

Use the links below to locate and identify the DNA sequence to use as the starting template for your target(s).

Query Tools

Ensembl ^{uswest.ensembl.org}

UC-SantaCruz ^{genome.ucsc.edu}

Comprehensive Databases

NCBI GenBank ^{ncbi.nlm.nih.gov/Genbank/}

Japan DDBJ ^{ddbj.nig.ac.jp}

SNP/Target Sequence Tool

uVariants ^dna-utah.org

Placement of Primers

Using the template, primers can be chosen by many tools. User-selected primers can be evaluated. We recommend PrimerBlast below for its versatility with Primer3 also solid and popular option.

LINKS

PrimerBlast ^{ncbi.nlm.nih.gov}

Primer3 ^{bioinfo.ut.ee}

PrimerSPY ^dna-utah.org

Assess Primers

The ability to differentiate primers and predict success is difficult. Assessing with a number of online tools can help.

BINDING

• BLAST ^{ncbi.nlm.nih.gov}

• In-Silico PCR ^{genome.ucsc.edu}

Characteristics such as Tm, GC%, Length

• Tm Tool ^dna-utah.org

• OligoAnalyzer ^idtdna.com

Dimerization

• MultiPrimer Analyzer ^{thermofisher.com}

• AutoDimer ^nist.gov

Predict Melting Behaviors

uMelt ^dna-utah.org

Melting Prediction ^{Stitchprofiles.uio.no}

POLAND ^{biophys.uni-duesseldorf.de}

Much appreciation to Eivind Tostesen and Gerhard Steger for their fantastic packages above.

Clustering HRM

MeltingPlot ^{Universitá degli Studi di Milano}