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VizPrimer: a web server for visualized PCR primer design based on known gene structure.

Identifieur interne : 000299 ( PubMed/Corpus ); précédent : 000298; suivant : 000300

VizPrimer: a web server for visualized PCR primer design based on known gene structure.

Auteurs : Yang Zhou ; Wubin Qu ; Yiming Lu ; Yanchun Zhang ; Xiaolei Wang ; Dongsheng Zhao ; Yi Yang ; Chenggang Zhang

Source :

Bioinformatics (Oxford, England) ; 2011.

RBID : pubmed:22016409

English descriptors

KwdEn :
- Animals, DNA Primers (genetics), Exons, Humans, Membrane Proteins (genetics), Mice, Nerve Tissue Proteins (genetics), Open Reading Frames, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Protein Isoforms (genetics).
MESH :
- chemical , genetics : DNA Primers, Membrane Proteins, Nerve Tissue Proteins, Protein Isoforms.
- Animals, Exons, Humans, Mice, Open Reading Frames, Polymerase Chain Reaction, Polymorphism, Single Nucleotide.

Abstract

The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs).

DOI: 10.1093/bioinformatics/btr582
PubMed: 22016409

Links to Exploration step

pubmed:22016409

Le document en format XML

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<author><name sortKey="Zhou, Yang" sort="Zhou, Yang" uniqKey="Zhou Y" first="Yang" last="Zhou">Yang Zhou</name>
<affiliation><nlm:affiliation>Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing 100850, China.</nlm:affiliation>
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<author><name sortKey="Qu, Wubin" sort="Qu, Wubin" uniqKey="Qu W" first="Wubin" last="Qu">Wubin Qu</name>
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<author><name sortKey="Lu, Yiming" sort="Lu, Yiming" uniqKey="Lu Y" first="Yiming" last="Lu">Yiming Lu</name>
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<author><name sortKey="Zhang, Yanchun" sort="Zhang, Yanchun" uniqKey="Zhang Y" first="Yanchun" last="Zhang">Yanchun Zhang</name>
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<author><name sortKey="Wang, Xiaolei" sort="Wang, Xiaolei" uniqKey="Wang X" first="Xiaolei" last="Wang">Xiaolei Wang</name>
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<author><name sortKey="Zhao, Dongsheng" sort="Zhao, Dongsheng" uniqKey="Zhao D" first="Dongsheng" last="Zhao">Dongsheng Zhao</name>
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<author><name sortKey="Yang, Yi" sort="Yang, Yi" uniqKey="Yang Y" first="Yi" last="Yang">Yi Yang</name>
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<author><name sortKey="Zhang, Chenggang" sort="Zhang, Chenggang" uniqKey="Zhang C" first="Chenggang" last="Zhang">Chenggang Zhang</name>
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<term>Exons</term>
<term>Humans</term>
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<front><div type="abstract" xml:lang="en">The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs).</div>
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<Abstract><AbstractText Label="SUMMARY" NlmCategory="CONCLUSIONS">The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs).</AbstractText>
<AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">VizPrimer is freely available at http://biocompute.bmi.ac.cn/CZlab/VizPrimer/. The web server supported browsers: Chrome (≥5.0), Firefox (≥3.0), Safari (≥4.0) and Opera (≥10.0).</AbstractText>
<AbstractText Label="CONTACT" NlmCategory="BACKGROUND">zhangcg@bmi.ac.cn; yangyi528@vip.sina.com.</AbstractText>
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VizPrimer: a web server for visualized PCR primer design based on known gene structure.

VizPrimer: a web server for visualized PCR primer design based on known gene structure.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki