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