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qPCR NEWSLETTER - March 2012 - focus on Primer Design Algorithms,
Databases & Resources
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Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time
PCR (qPCR
and RT-qPCR), which are compiled and summarised on the
Gene Quantification homepage. The focus of this newsletter issue is:

* 10th anniversary of our web portal  - http://www.Gene-Quantification.info
from March 2002 to March 2012
* Importance of primer design - Primer Design Algorithms, Databases &
Resources http://Primers.gene-quantification.info
* Follow ou new established "GeneQuan Daily NEWS" - a daily updated
newsletter - http://Daily-News.gene-quantification.info


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This month we celebrate the 10th anniversary of our Gene
Quantification web portal.
We started in March 2002 with 1,500 visitors and in 2012 we are proud
to welcome more than 100,000 readers per month!
Follow our history => http://page-statistics.gene-quantification.info

Many thanks to all our readers

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages


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Importance of primer design - Primer Design Algorithms, Databases &
Resources
http://Primers.gene-quantification.info

For primer design the sequence of the gene of interest and the primer
design software
is needed, which can calculate possible primer pairs regarding the
detection system.
In theory this is simple but often the calculated primer pairs do not
work in PCR.
Therefore optimization of the primer design or the amplification
protocol is necessary.
Primer design is the most critical step in qPCR analysis, because
specificity, efficiency
and accuracy of the assay are influenced. Therefore primer design
should be done
carefully, to avoid any primer dimers or unwanted reaction artefacts.
Initially this
may be laborious and time consuming, but after failure an additional
primer pair
redesign and ordering becomes very fretful.

Reference:  Chapter 5 - RT-PCR Optimisation Strategies by M Reiter &
MW. Pfaffl,
in PCR Troubleshooting and Optimization - The Essentail Guide
edited by Suzanne Kennedy & Nick Oswald


Primer design tools Real-time PCR primer & probe databases

* RTPrimerDB: the portal for real-time PCR primers and probes
* BiSearch: primer-design and search tool for PCR on bisulfite-treated
genomes
* PRaTo: A web-tool to select optimal primer pairs for qPCR
* AutoDimer: a screening tool for primer-dimer and hairpin structures
* A PCR primer bank for quantitative gene expression analysis
* A comprehensive collection of experimentally validated primers for
Polymerase Chain
Reaction quantitation of murine transcript abundance
* PrimerBank: a PCR primer database for quantitative gene expression
analysis, 2012 update
* GETPrime: a gene- or transcript-specific primer database for
quantitative real-time PCR
* methBLAST and methPrimerDB: web-tools for PCR based methylation
analysis
* AtRTPrimer: database for Arabidopsis genome-wide homogeneous and
specific RT-PCR primer-pairs


Real-time PCR primer design tools

* RExPrimer: an integrated primer designing tool increases PCR
effectiveness by avoiding
3' SNP-in-primer and mis-priming from structural variation
* BatchPrimer3: a high throughput web application for PCR and
sequencing primer design
* Java web tools for PCR, in silico PCR, and oligonucleotide assembly
and analysis
* ConservedPrimers 2.0: a high-throughput pipeline for comparative
genome referenced
intron-flanking PCR primer design and its application in wheat SNP
discovery
* PriSM: a primer selection and matching tool for amplification and
sequencing of viral genomes
* PCRTiler: automated design of tiled and specific PCR primer pairs
* maxAlike: maximum likelihood-based sequence reconstruction with
application to
improved primer design for unknown sequences
* PrimerIdent: A web based tool for conserved primer design
* ThermoPhyl: a software tool for selecting phylogenetically optimized
conventional
and quantitative-PCR taxon-targeted assays for use with complex
samples
* WASP: a Web-based Allele-Specific PCR assay designing tool for
detecting SNPs and mutations

download the papers here => http://Primers.gene-quantification.info


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Follow our new established "GeneQuan Daily NEWS"
A daily updated newsletter around Gene Quantification and qPCR  -
http://Daily-News.gene-quantification.info


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Please forward this qPCR NEWS
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to further scientists and friends who are interested in qPCR !

Best regards,
Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

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please use following
LINK http://qPCRnews.gene-quantification.info/


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The qPCR NEWS and the Gene Quantification Pages are educational sites
with the only
purpose of facilitating access to qPCR related information on the
internet. The qPCR
NEWS and the Gene Quantification Pages are edited by Michael W.
Pfaffl.
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