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MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research

Overview of attention for article published in Clinical Epigenetics, March 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (88th percentile)
  • High Attention Score compared to outputs of the same age and source (94th percentile)

Mentioned by

news
1 news outlet
twitter
9 tweeters

Citations

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5 Dimensions

Readers on

mendeley
31 Mendeley
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1 CiteULike
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Title
MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research
Published in
Clinical Epigenetics, March 2016
DOI 10.1186/s13148-016-0190-9
Pubmed ID
Authors

Ram Vinay Pandey, Walter Pulverer, Rainer Kallmeyer, Gabriel Beikircher, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel

Abstract

Methylation-sensitive restriction enzymes-polymerase chain reaction (MSRE-PCR) has been used in epigenetic research to identify genome-wide and gene-specific DNA methylation. Currently, epigenome-wide discovery studies provide many candidate regions for which the MSREqPCR approach can be very effective to confirm the findings. MSREqPCR provides high multiplexing capabilities also when starting with limited amount of DNA-like cfDNA to validate many targets in a time- and cost-effective manner. Multiplex design is challenging and cumbersome to define specific primers in an effective manner, and no suitable software tools are freely available for high-throughput primer design in a time-effective manner and to automatically annotate the resulting primers with known SNPs, CpG, repeats, and RefSeq genes. Therefore a robust, powerful, high-throughput, optimized, and methylation-specific primer design tool with great accuracy will be very useful. We have developed a novel pipeline, called MSRE-HTPrimer, to design MSRE-PCR and genomic PCR primers pairs in a very efficient manner and with high success rate. First, our pipeline designs all possible PCR primer pairs and oligos, followed by filtering for SNPs loci and repeat regions. Next, each primer pair is annotated with the number of cut sites in primers and amplicons, upstream and downstream genes, and CpG islands loci. Finally, MSRE-HTPrimer selects resulting primer pairs for all target sequences based on a custom quality matrix defined by the user. MSRE-HTPrimer produces a table for all resulting primer pairs as well as a custom track in GTF file format for each target sequence to visualize it in UCSC genome browser. MSRE-HTPrimer, based on Primer3, is a high-throughput pipeline and has no limitation on the number and size of target sequences for primer design and provides full flexibility to customize it for specific requirements. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 190 primer pairs, 71 % could be successfully validated. The MSRE-HTPrimer software is freely available from http://sourceforge.net/p/msrehtprimer/wiki/Virtual_Machine/ as a virtual machine.

Twitter Demographics

The data shown below were collected from the profiles of 9 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 31 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Ireland 1 3%
Unknown 30 97%

Demographic breakdown

Readers by professional status Count As %
Researcher 7 23%
Student > Bachelor 6 19%
Student > Master 5 16%
Student > Ph. D. Student 3 10%
Professor > Associate Professor 2 6%
Other 5 16%
Unknown 3 10%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 11 35%
Agricultural and Biological Sciences 6 19%
Medicine and Dentistry 3 10%
Computer Science 2 6%
Engineering 2 6%
Other 1 3%
Unknown 6 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 March 2019.
All research outputs
#1,233,684
of 14,561,844 outputs
Outputs from Clinical Epigenetics
#69
of 765 outputs
Outputs of similar age
#30,634
of 268,172 outputs
Outputs of similar age from Clinical Epigenetics
#1
of 18 outputs
Altmetric has tracked 14,561,844 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 91st percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 765 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.7. This one has done particularly well, scoring higher than 90% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 268,172 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 88% of its contemporaries.
We're also able to compare this research output to 18 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 94% of its contemporaries.