External Tools

Collect Sequences

Use the following links to find SNPs and establish the DNA template for each target.

Sequence Query Tools

Ensembl ^{uswest.ensembl.org}

UC-SantaCruz ^{genome.ucsc.edu}

HGNC (Human Gene) ^{genenames.org}

HGVS (Variant) ^{hgvs-nomenclature.org}

Comprehensive Databases

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

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

ENCODE ^{encodeproject.org}

INSDC ^insdc.org

Variants

dbSNP ^{ncbi.nlm.nih.gov}

HGMD ^{hgmd.cf.ac.uk}

ClinVar ^{ncbi.nlm.nih.gov}

gnomAD ^{gnomad.broadinstitute.org}

ISGR ^{internationalgenome.org}

OMIM ^omim.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 a solid and popular option.

LINKS

PrimerBlast ^{ncbi.nlm.nih.gov}

Primer3 ^{primer3plus.com}

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

Much appreciation to Eivind Tostesen and Gerhard Steger for their fantastic packages (Stitchprofiles and POLAND).

Clustering HRM

MeltingPlot ^{Universitá degli Studi di Milano}