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Primer Blast logo
online PCR primer design
Subcategories: NCBI
Primer Blast allows: to design PCR primers

Primer Blast is a web application that uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. The blast results are then automatically analyzed to avoid primer pairs that can cause amplification of targets other than the input template.

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PCR Now logo
A Real-Time PCR Primer Design Tool

PCR Now permits to design Real-Time Polymerase Chain Reaction (RT-PCR) primers for any number of user-defined coding sequences. Great control over primer properties.

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The goal of iCODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers) is to simplify the process of designing degenerate PCR primers by integrating both new and existing bioinformatics tools into an interactive, Open Source, Web application. This beta version of the new program is currently available to interested researchers for free. In addition to simplifying degenerate primer design workflows, iCODEHOP extends and improves the CODEHOP method of designing degenerate PCR primers from pro

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OligoCalc logo
an online oligonucleotide properties calculator

OligoCalc is a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar ‘calculator’ look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating

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Primer3 Plus logo

Primer3 Plus is the new improved web interface to the popular Primer3 primer design program.

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QuantPrime logo

QuantPrime is very user-friendly tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is ready to use with most publicly available eukaryotic transcriptomes, including all higher eukaryote model organisms and important plant crops, while benefiting from exon-intron border and splice variant information in available genome annotations.

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RAPD primer generator logo

Description not available.

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IDT logo
IDT allows: IDT

A very intuitive tool to design primer. The request need the entering of gene sequence or sequence of interest (multiple sequences in FASTA format with exons in uppercase letters and introns in lowercase letters, positive orientation). A complete tutorial is available.

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PrimacladeP logo

PrimacladeP accepts a multiple species nucleotide alignment file as input and identifies a set of PCR primers that will bind across the alignment.

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Primerquest logo
Primerquest allows: IDT

IDT's PrimerQuest is a web application to design PCR primers based on Primer3 software.

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PriFi logo

Upload a file containing Fasta-formatted DNA sequences or alternatively a *.aln file, select the control one wants over the primer design from an extensive list

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Primer3 logo

Primer3 is a very powerful PCR primer design online application permitting one considerable control over the nature of the primers, including size of product desired, primer size and Tm range, and presence/absence of a 3’-GC clamp.

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QuikChange Primer Design logo
primer design for mutagenesis experiments

The QuikChange® Primer Design Program provides primer design for mutagenesis experiments. Using primer design guidelines described in QuikChange manuals, this online program calculates and designs the appropriate primer sequences with the optimal melting temperature.

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GeneFisher2 logo

GeneFisher2 is a very good site allowing great control over primer design

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Exon Primer logo

ExonPrimer is a web application that helps to design intronic primers for the PCR amplification of exons. The script needs a cDNA and the corresponding genomic sequence as input. It aligns these sequences using Blat and designs PCR primers to amplify each exon using Primer3. The positions of the exons are deduced from the alignment of the genomic and the cDNA sequences. Insertions/deletions up to 6 base pairs are bridged by postprocessing. Exons with small introns in-between are combined. Exons

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Quantitative PCR Primer Database logo

The Quantitative PCR Primer Database (QPPD) provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RT–PCR) assays. All data has been gathered from published articles, cited in PubMed. Searching in the QPPD you will find: primer sets and probes for a given gene, primer location, amplicon size, assay type, positions of single nucleotide polymorphisms (SNPs), literature references, available I.M.A.G.E.

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