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ASePCR -- alternative splicing electronic RT–PCR in multiple tissues and organs
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| Carry out simulated RT-PCR to detect transcript variants.
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Academic and Industrial Information Platform for qPCR
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| Search for comprehensive information on qPCR related technologies, products, vendors and services.
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Amplicon --software for designing PCR primers on aligned DNA sequences
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| Design PCR primers on aligned groups of DNA sequences.
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Assembly PCR oligo maker -- a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production
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| Design of oligodeoxynucleotides for the PCR based construction of long DNA molecules.
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AutoDimer -- a screening tool for primer-dimer and hairpin structures
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| Examine multiple PCR primers for primer-dimer and hairpin structures.
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BatchPrimer3 -- a high throughput web application for PCR and sequencing primer design
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| Design different types of PCR primers and sequencing primers in a high-through manner.
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CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design
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| Design degenerate PCR primers based on multiple protein sequences alignments.
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DNA Methylation analysis PCR Primer Database
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| Search for validated PCR primers for DNA methylation analysis.
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DNA and Protein Sequence Manipulation Suite 2
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| Conduct a variety of analysis of DNA and protein sequences. |
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DePIE -- Designing Primers for Protein Interaction Experiments
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| Design PCR primers for protein-protein interaction experiments.
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EasyExonPrimer -- automated primer design for exon sequences
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| Design PCR primers for large-scale resequencing of exons.
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GeMprospector —- online design of cross-species genetic marker candidates in legumes and grasses
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| Design PCR primers to amplify sets of cross-species genetic marker candidates targeting either legumes or grasses.
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Gene2Oligo -- Oligonucleotide Design for in vitro Gene Synthesis
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| Design oligonucleotides to support the development of in vitro gene synthesis.
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Greene SCPrimer -- a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
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| Design degenerate PCR primers for large groups of related DNA sequences.
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IDT SciTools -- a suite for analysis and design of nucleic acid oligomers
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| Advanced Oligo Design and Analysis.
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IMGT/PRIMER-DB -- Immunogenetics oligonucleotide primer database
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| Search for information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).
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MFEprimer -- multiple factor evaluation of the specificity of PCR primers
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| Evaluate the specificity of PCR primers.
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MSY Breakpoint Mapper -- a database of sequence-tagged sites for defining naturally occurring deletions in the human Y chromosome
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| A database of sequence-tagged sites (STSs) and a user interface for mapping partial deletions in the male-specific region of the human Y chromosome (MSY).
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MethPrimer - Design Primers for Methylation PCRs
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| Design PCR primers for methylation PCR.
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Molecular Probe Data Base (MPDB)
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| Search information on molecular probes and synthetic oligonucleotides that had proven useful in real experimental conditions.
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MuPlex -- multi-objective multiplex PCR assay design
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| Design multiplex PCR assays.
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Multiple sequence alignment of prokaryotic 16S rDNA
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| Examine the comprehensive database of 16S rDNA prokaryotic multiple sequence alignment. |
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MutScreener -- primer design tool for PCR-direct sequencing
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| Design primers for PCR-direct sequencing project.
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NTMG (N-terminal Truncated Mutants Generator for cDNA) -- An automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants
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| Use this web-based application system to apply the sequential deletion method to locate the functional domain of a protein and generate groups of primers.
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NetPrimer
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| Analyze primers for melting temperature, secondary structures including hairpins, self-dimers, and cross-dimers in primer pairs.
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NormFinder -- tool for identifying normalization genes
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| Identify the optimal normalization gene among a set of candidates.
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OHM -- OligoHeatMap
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| An online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.
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OligoArrayDb -- pangenomic oligonucleotide microarray probe sets database
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| A comprehensive database containing pangenomic oligonucleotide microarray probe sets.
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OligoCalc -- An online oligonucleotide properties calculator
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| Calculate 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.
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OligoDesign -- optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling
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| Design optimal LNA (locked nucleic acid) substituted oligonucleotides for functional genomics applications.
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PRIMEGENS -- robust and efficient design of gene-specific probes for microarray analysis
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| Select gene-specific fragments and then design PCR primer pairs to amplify fragments suitable for microarray probes.
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PROBEmer
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| Selects optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays.
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PUNS -- transcriptomic- and genomic-in silico PCR for enhanced primer design
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| Design PCR primers with high specificity.
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PerlPrimer -- cross-platform, graphical primer design for standard, bisulphite and real-time PCR
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| Design various PCR primers on PC, Mac or Linux based system.
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PriFi -- using a multiple alignment of related sequences to find primers for amplification of homologs
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| Design PCR primers based on multiple sequence alignment of homologous DNA sequences.
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Primaclade -- a flexible tool to find conserved PCR primers across multiple species
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| Find conserved PCR primers across multiple species based on a multiple nucleotide alignments.
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Primaclade -- a flexible tool to find conserved PCR primers across multiple species
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| Design PCR primers based on the alignment of DNA sequences from multiple species.
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Primer Design Assistant (PDA) -- a web-based primer design tool
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| Design and evaluate PCR primers.
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Primer Nerd
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| Use Primer3 algorithm to batch design PCR primers for Fluorescence Polarization (FP) experiments.
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Primer3 -- An online tool for PCR primer design
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| Design optimum PCR primers from nucleotide sequences.
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Primer3Plus -- An enhanced web interface to Primer3
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| Design PCR primers with this easy to use and powerful new web interface for Primer3.
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PrimerPCR -- PCR primers for eukaryotic and prokaryotic genes
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| Search for pre-designed and tested PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes.
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PrimerStation -- a highly specific multiplex genomic PCR primer design server for the human genome
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| Design highly specific and accurate multiplex genomic PCR primer for human genome.
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PrimerX -- Automated design of mutagenic primers for site-directed mutagenesis
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| Design PCR primers for site-directed mutagenesis using DNA or protein sequences.
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PrimerZ -- Streamlined primer design for promoters, exons and human SNPs
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| Design primers for genes and human SNPs.
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Probewiz
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| Design PCR primers for amplifying probes for cDNA arrays, with the goal of reducing or eliminating cross-hybridizations.
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Projector 2 -- contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies
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| Automatically position contigs from an unfinished prokaryotic genome onto (parts of) a template genome of a closely related strain or species in order to close a significant number of remaining gaps in the late stages of a genome sequencing project.
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QPPD -- Quantitative PCR Primer Database for human and mouse
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| Search for published Quantitative PCR Primer for studying of human and mouse mRNA.
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QPRIMER -- a quick web-based application for designing conserved PCR primers from multigenome alignments
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| Design conserved genomic PCR and RT-PCR primers from multigenome alignments targeting specific exons or introns.
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QUMA -- quantification tool for methylation analysis
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| Align, visualize and quantify
bisulfite sequence data for CpG methylation analysis.
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RTPrimerDB -- The Real-Time PCR primer and probe database
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| Search for validated real time PCR primer and probe sequences.
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SNP Cutter -- a comprehensive tool for SNP PCR–RFLP assay design
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| Design PCR–RFLP assays on a batch of SNPs from the human genome.
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SNPbox -- Web-based High-throughput Primer Design from Gene to Genome
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| Automatically design PCR primers for large-scale amplification and sequencing projects aimed at constructing single nucleotide polymorphisms (SNPs) maps.
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SNPrimers -- Map and plot primers to amplicons of SNPs (batch) - especially useful for Pyrosequencing assay design
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| Evaluated SNP genotyping primers by mapping primers to (batch) SNPs' amplicons/gDNA sequence.
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SNPsFinder -- a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes
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| Conduct genome-wide identification of SNPs in microorganisms. |
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SOP3 v2 -- web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms
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| Design PCR primers for genotyping assays and SNP detection.
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SSRPrimer and SSR Taxonomy Tree -- Biome SSR discovery
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| Find Simple sequence repeats and design PCR primers for subsequent amplification.
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SeqMap -- mapping massive amount of oligonucleotides to the genome
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| A tool For mapping millions of short sequences to the genome.
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Snap -- an integrated SNP annotation platform
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| Perform gene specific SNPs analysis for human genes. |
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Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays
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| Optimize the selection of microbial forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input. |
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Swiss EMBnet node web server
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| Use a collection of bioinformatics tools at this portal site. |
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TRDB — The Tandem Repeats Database
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| Search for various information and analyze repeats in genomic DNA. |
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The PCR Suite
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| Use this suite of programs to design different types of PCR primers.
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The PCR suite
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| Design of primer sets encompassing single nucleotide polymorphisms (SNPs), all exons of a single gene, all open reading frames in a list of cDNAs or the creation of overlapping PCR products.
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UCSC In-Silico PCR
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| Map the locations of a pair of PCR primers in the genome of a model organism.
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VNTRDB -- a bacterial variable number tandem repeat locus database
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| Search for sequence information on microbial Variable number tandem repeats. |
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VectorNTI Suite Version 10 (free to nonprofit users)
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| Design and analyze primers for different types of PCR-based amplifications.
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VirOligo -- a database of virus-specific oligonucleotides
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| Search for virus specific oligonucleotides. |
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dnaMATE -- a consensus melting temperature prediction server for short DNA sequences
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| Calculate a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts).
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ePCR
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| search DNA sequences for sequence tagged sites (STSs.
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geNorm -- Tools for normalization of real-time qRT-PCR data
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| Accurately normalize the real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
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methBLAST -- a web tool for DNA methylation analysis
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| Find primer binding sites and analyze specificity of PCR based assays that use bisulfite converted DNA as input material, including bisulfite sequencing, methylation-specific PCR (MSP), combined bisulfite restriction analysis (COBRA), bisulfite-PCR-SCCP (BiPS), methylation-sensitive single-nucleotide primer extension (Ms-SNuPE).
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probeBase -- An online resource for rRNA-targeted oligonucleotide probes
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| Search for published rRNA-targeted oligonucleotide probe sequences. |
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probeCheck -- a central resource for evaluating oligonucleotide probe coverage and specificity
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| Evaluate probe and primer specificity.
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qPrimerDepot -- a primer database for quantitative real time PCR of human Refseq.
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| Search for qRT PCR primers for human RefSeq sequences.
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qPrimerDepot -- a primer database for quantitative real time PCR of mouse RefSeq
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| Search for qRT PCR primers for mouse RefSeq sequences.
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