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qPCR newsletter
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editor@gene-quantificatio
medicine forum beginner


Joined: 11 Apr 2005
Posts: 8

PostPosted: Wed May 03, 2006 11:34 am    Post subject: qPCR newsletter Reply with quote

Dear researcher,
dear Gene Quantification page reader,

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

- qPCR Data Analysis and qPCR Software Applications
- new qPCR reviews and interesting papers
- BabelFish translation service
- updated qPCR Event calendar 2006

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Please visit our independent Academic & Industrial Information qPCR
Platform - The reference in qPCR!

A lot of qPCR companies and independent insitutions participate in our
qPCR information platform. On the company sub-pages new real-time
cyclers, consumables, new released kits and detection chemistries, as
well as innovative amplification technologies are presented. Links from
the sub-pages will lead you to the related product pages at the
respective homepage. You are welcome to join our Academic & Industrial
qPCR platform with your company or institution !

For further info please contact
qPCRplatform@gene-quantification.info

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REST 2005 version (version 1.9.12 released April 2006)

Download => Manual REST 2005 version 1.9.12

Download => REST 2005 software

http://www.gene-quantification.de/rest-2005.html

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qCalculator version 1.0

Tool to calculate relative mRNA Gene Expression in real-time PCR.
programmed by Ralf Gilsbach, Institut of Pharmacology & Toxicology,
University of Bonn

Short qCalculator description
Download software

http://www.gene-quantification.de/download.html#qcalculator

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qPCR-DAMS - A Database Tool to Analyze, Manage, and Store Both Relative
and Absolute Quantitative Real-Time PCR data.
Jin N, He K, Liu L.; Physiol Genomics. 2006
Physiological Sciences, Oklahoma State University, Stillwater, OK, USA.

Quantitative real-time PCR is an important high throughput method in
biomedical sciences. However, existing software has limitations in
handling both relative and absolute quantification. We designed
qPCR-DAMS (Quantitative PCR Data Analysis and Management System), a
database tool based on Access 2003, to deal with such shortcomings by
the addition of integrated mathematical procedures. qPCR-DAMA allows a
user choose among four methods for data processing within a single
software package: (I) Ratio relative quantification, (II) Absolute
level, (III) Normalized absolute expression, and (IV) Ratio absolute
quantification. qPCR-DAMS also provides a tool for multiple reference
gene normalization. qPCR-DAMS has three quality control steps and a
data display system to monitor data variation. In summary, qPCR-DAMS is
a handy tool for real-time PCR users.

http://www.gene-quantification.de/main-bioinf.shtml#qpcr-dams

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qPCR data analysis software

- qBase - management and automated analysis of real time qPCR data
- DART PCR version 1.0
- GENEX Software by Bio-Rad
- qGENE Software
- SoFAR Software
- geNorm software
- BestKeeper software

More Info => http://bioinformatics.gene-quantification.info/

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ePCR - A web server for performing electronic PCR

by Kirill Rotmistrovsky, Wonhee Jang and Gregory D. Schuler

National Center for Biotechnology Information, National Library of
Medicine, National Institutes of Health, Bethesda, MD 20984, USA

http://www.gene-quantification.de/main-bioinf.shtml#epcr

'Electronic PCR' (e-PCR) refers to a computational procedure that
is used to search DNA sequences for sequence tagged sites (STSs), each
of which is defined by a pair of primer sequences and an expected PCR
product size. To gain speed, our implementation extracts short
'words' from the 3' end of each primer and stores them in a sorted
hash table that can be accessed efficiently during the search. One
recent improvement is the use of overlapping discontinuous words to
allow matches to be found despite the presence of a mismatch. Moreover,
it is possible to allow gaps in the alignment between the primer and
the sequence. The effect of these changes is to improve sensitivity
without significantly affecting specificity. The new software provides
a search mode using a query STS against a sequence database to augment
the previously available mode using a query sequence against an STS
database. Finally, e-PCR may now be used through a web service, with
search results linked to other web resources such as the UniSTS
database and the MapViewer genome browser. The e-PCR web server may be
found at www.ncbi.nlm.nih.gov/sutils/e-pcr

--------------------------------------------------------------------------------

iPCR = Virtual PCR

http://www.ch.embnet.org/software/iPCR_form.html

http://www.gene-quantification.de/main-bioinf.shtml#ipcr

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NEW REVIEWs

The real-time polymerase chain reaction.
Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonak J, Lind K,
Sindelka R,
Sjoback R, Sjogreen B, Strombom L, Stahlberg A, Zoric N.; Mol Aspects
Med. 2006 (2-3): 95-125.

SPUD: a quantitative PCR assay for the detection of inhibitors in
nucleic acid
preparations.
Nolan T, Hands RE, Ogunkolade W, Bustin SA.; Anal Biochem. 2006 351(2):
308-310

Real-time reverse transcription PCR and the detection of occult disease
in colorectal cancer.
Bustin SA, Mueller R. Mol Aspects Med. 2006 27(2-3): 192-223

Faster quantitative real-time PCR protocols may lose sensitivity and
show increased variability. Hilscher C, Vahrson W, Dittmer DP. Nucleic
Acids Res. 2005 33(21): e182.

Comparison of in vitro and in vivo reference genes for internal
standardization ofreal-time PCR data.
Gilsbach R, Kouta M, Bonisch H, Bruss M. Biotechniques. 2006 40(2):
173-177

http://www.gene-quantification.de/real-time.html#newpub

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TRANSLATOR - DIRECTORY

An Alta Vista BabelFish translation service of our English written Gene
Quantification homepage is NOW available for all sub-pages.

Translation of the page content can be performed from English to
Chinese, German, Japanese, Korean, French, Italian, Portuguese and
Spanish.

http://www.gene-quantification.de/body.html#translator

A lot of links and keywords are listed in our DIRECTORY

http://directory.gene-quantification.info/

--------------------------------------------------------------------------------

Upcoming Events World-wide academic and commercial qPCR Events are
listed at events.gene-quantification.info

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars,
qPCR Education Program.....etc.
submit your qPCR event here events@gene-quantification.info

--------------------------------------------------------------------------------

TATAA Biocenter Germany qPCR Application workshops:

http://tataa.gene-quantification.info/

TATAA Biocenter have found that the worldwide demand for training in
the field of quantitative real-time PCR (qPCR) is huge. To coordinate
this we aim to arrange practical courses, e.g. 3-day Core Module and
1-day or 2-day Biostatistics Module:

The basic qPCR Core Module contains three workshop days:
First workshop day will be directed to people planning or considering
using qPCR in their research and also users not yet fully familiar will
quantitative PCR. Second day targets more advanced users and people
concentrating on different quantification strategies. The third day
focuses on aspects in sample preparation and reverse transcription. The
additional qPCR Biostatistics Module explains statistics applicable to
qPCR and teaches how to use statistics to interpret qPCR gene
expression data, and classify samples based on qPCR expression
profiling.
Courses contain both, theoretical seminars and practical hands-on
training with experienced supervision. Practical training will be
performed on three different real-time PCR cyclers, using multiple
detection chemistries. The Biostatistics Module is further based on
computer-based demonstrations. Please bring your own Laptop !
qPCR courses are held in regularly in Göteborg, Sweden and in
Freising-Weihenstephan, Germany (near Munich, very close to the Munich
Airport - MUC). Depending on the occasion different prices may apply.
Also different course modules are available on the different occasions.
Further customized workshops and specialized trainings will be held as
well across Europe and world-wide. TATAA Biocenter Germany courses are
held in cooperation with the Institute of Physiology, located at the
Technical University of Munich, in Freising-Weihenstephan.

Workshop details => 3-days core module
Download => short qPCR basic course description at the TATAA Biocenter
Germany
Location => world-wide access to TATAA Biocenter Germany in Freising
Weihenstephan
Download Map => local access to TATAA Biocenter Germany (map of
Freising-Weihenstephan)
Lab View => some photos of our lab equipment
Registration => TATAA Biocenter Workshops (Germany and world-wide)
Course Occasions 2006:
16th - 19th May 2006 ( fully booked )
27th - 30th June 2006 ( still availibility )
25th - 29th September 2006
23rd - 27th October 2006
20th - 24th November 2006

--------------------------------------------------------

Please send the qPCR NEWS to further scientists and friends who are
interested in qPCR and in our Academic & Industrial Information
Platform for qPCR.

best regards

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
http://www.gene-quantification.info

--------------------------------------------------------

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 and powered by BioScience Events
www.BioScience-Events.com Copyright İ 2005 -2006 BioScience Events.
All rights reserved. Any unauthorized use, reproduction, or transfer
of this message or its contents, in any medium, is strictly prohibited.
Disclaimer & Copyrights are displayed on the homepage
www.gene-quantification.com To subscribe or change your e-mail
address in qPCR NEWS, and if you would like to receive future issues
FREE of charge, please send an e-mail with the subject SUBSCRIBE to
mailto:newsletter@gene-quantification.info?subject=SUBSCRIBE
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