Israel Science and Technology Directory

Biomedical : Online Tools for Primer Design and Analysis

Online ToolDescription
AutoPrimePrimer design for real-time PCR measurement of eukaryotic gene expression.
Dicer-Substrate siRNAGenerates DsiRNAs for any sequence from any species.
Genomic PrimersInput form for creating primers around exons in genomic DNA. For primer design, the Primer3 program is used.
IDT Oligo AnalyzerOnline calculation of oligonucleotide parameters such as melting temperature. Shows self-dimers, hairpin, and performs Blast.
IDT PrimerQuestPrimer and probe design and selection.
NetPrimerJava applet for primer design.
Primer-BLASTFinding primers specific to PCR template (using Primer3 and BLAST).
Primer1Primer design for tetra-primer ARMS-PCR. PCR designer for restriction analysis of sequence mutations.
Primer3Utility for locating oligonucleotide primers for PCR amplification of DNA sequences.
PrimerXAutomated design of mutagenic primers for site-directed mutagenesis.
Primo ProPCR Primer Design.
QuantPrimeAutomatic high-throughput primer pair design and specificity testing for realtime qPCR on any organism.
RF-CloningOnline tool for the design of primers for restriction-free cloning projects.
SFOLDSoftware for Statistical Folding of Nucleic Acids and Studies of Regulatory RNAs
UCSC In-Silico PCRIn-Silico PCR searches a genome sequence database with a given pair of PCR primers.
Web PrimerPrimer design and sets for amplifying yeast ORFs.
primers4cladesDesign of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages.

Primer Design Considerations

Desired characteristics of automated DNA sequencing primer design.