小中大【求助】PCR Primer design and PCR setup
pcr Primer design and PCR setupDesign of PCR and Sequencing Primers and PCR reactions
Design of Primers for Automated Sequencing
PCR Bioinformatics and Web based primer design
PCR links at Bioinformatics.Net
Primer Design Workshop
Probe/ primer design software
Primer design webservers for PCR, mutagenesis and RNAi
AntiSense Design - Design antisense primers at IDT
AutoPrime - designs primers that are specific for expressed sequences (mRNA).
BatchPrimer3 - High throughput web application for PCR and sequencing primer design
CODEHOP- COnsensus-DEgenerate Hybrid Oligonucleotide Primers
Exonprimer - Design primers for the amplification of exons with intronic primers
Genefisher - Interactive PCR primer design
MEDUSA - A tool for automatic selection and visual assessment of PCR primer pairs (Karolinska)
Methprimer - Design primers for methylation PCR
mPrimer3 - modified Primer3
MutScreener - Design primers for mutation screening (by PCR-direct sequencing)
NetPrimer - Free primer design service of Premier Biosoft.
Oligodb - a web-based system for interactive design of oligo DNA for transcription profiling (hybridization) of human genes. The oligodb system uses the human DNA-transcripts of ENSEMBL. Reference [PubMed][pdf]
Osprey - Oligonucleotide Design Software for Sequencing and Gene Expression
PCR suite - a collection of programs to search overlapping primers, genomic primers for exon amplification, SNP- and cDNA flanking primers
PRIDE - The less automated webversion of PRIDE (a.o. 50-70 mer oligo design)
Primaclade - a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of PCR primers that will bind across the alignment.
Primer3 - a common used software for designing primers
Primer3Plus - Use primer3 to pick primers for specific tasks
PrimerQuest - Primer design at IDT
Primer Generator - Automated generator of primers for site-directed mutagenesis
PrimerStation - multiplex human PCR primer design site
PrimerX - Automated design of primers for site-directed mutagenesis
[url=http://cgi-cuturl('www.daimi.au.dk/cgi-chili/primique/front.py')]Primique[/url] - Automatic design of specific PCR primers for each sequence in a family
Primo Unique - Primo Unique finds multiple primer pairs, each uniquely amplify one gene in a family.
ProbeWiz Server- The CBS ProbeWiz WWW server predicts optimal PCR primer pairs for generation of probes for cDNA arrays. Reference [PubMed]
PUNS - Primer-UniGene Selectivity Testing - compares primer sequences against the both the genome and transcriptome to assess the potential for multiple amplicons (Free registration required)
RNAi Design - Design primers for RNAi at IDT
ROSO - Software to design optimized oligonucleotide probes (size over 25 nucleotides) for microarrays
Sirna - Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design
SNPbox - a modular software package that automates the design of PCR primers for large-scale amplification and sequencing projects in a standardized manner resulting in high quality PCR amplicons with a low failure rate.
SNP Cutter SNP PCR-RFLP Assay Design. Primer design for restriction analysis of single nucleotide polymorphisms
Soligo - Target accessibility prediction and rational design of antisense oligonucleotides and nucleic acid probes
SOP3 - Selection of Oligonucleotide Primers for PCR and Pyrosequencing
SPADS - Specific Primers & Amplicon Design Software for amplification of individual members of gene familiesPCR Primer design software for local installationFreely available
Amplify - a freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs).
AmplifX - Software to test, manage and design your primers for Macintosh and Windows.
Fast PCR - PCR primer design, DNA and protein tools, repeats and own database searches
MEDUSA - A tool for automatic selection and visual assessment of PCR primer pairs (Karolinska)
Methyl Primer Express - free Applied Biosystems software to design high quality PCR primers for methylation mapping experiments.
MutaPrimer - Designs primers for Stratagene's QuikChange site directed mutagenesis kits.
OligoPicker - OligoPicker picks specific oligos by skipping regions with contiguous bases common in other sequences. In addition, oligo specificity is double-checked by NCBI BLAST. Sequence regions similar to non-coding RNAs are avoided because total RNA is often used for array hybridization. Low-complexity regions are also filtered out to maintain oligo specificity. Oligos and sequence regions that may form secondary structures are discarded since both the probes and the sequence target sites should be easily accessible for hybridization. Reference [PubMed]
PRIMEGENS- PRIMEGENS (PRIMEr Design Using GEN Specific Fragments) is a computer program to select gene-specific fragments and then design primer pairs using Primer3 for PCR amplifications. Reference [PubMed]
PrimerD - The primerD program implements a novel algorithm for the design of unique degenerate primer pairs.
Primer3 - a common used software for designing primers for microarray construction.
mPrimer3 - modified Primer3
ProMide - ProMide is a collection of command-line tools for Probe selection and Microarray Design.
STACKdb - The STACKdb, Sequence Tag Alignment and Consensus Knowledgebase, is generated by processing EST and mRNA sequences obtained from Genbank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACKdb database is created using tools called "stackPACK". Not freely available or commercial packages
