VizPrimer: a web server for visualized PCR primer design based on known gene structure.
Identifieur interne : 000A41 ( Main/Exploration ); précédent : 000A40; suivant : 000A42VizPrimer: a web server for visualized PCR primer design based on known gene structure.
Auteurs : Yang Zhou [République populaire de Chine] ; Wubin Qu ; Yiming Lu ; Yanchun Zhang ; Xiaolei Wang ; Dongsheng Zhao ; Yi Yang ; Chenggang ZhangSource :
- Bioinformatics (Oxford, England) ; 2011.
English descriptors
- KwdEn :
- 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
Affiliations:
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Le document en format XML
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last="Lu">Yiming Lu</name></author><author><name sortKey="Zhang, Yanchun" sort="Zhang, Yanchun" uniqKey="Zhang Y" first="Yanchun" last="Zhang">Yanchun Zhang</name></author><author><name sortKey="Wang, Xiaolei" sort="Wang, Xiaolei" uniqKey="Wang X" first="Xiaolei" last="Wang">Xiaolei Wang</name></author><author><name sortKey="Zhao, Dongsheng" sort="Zhao, Dongsheng" uniqKey="Zhao D" first="Dongsheng" last="Zhao">Dongsheng Zhao</name></author><author><name sortKey="Yang, Yi" sort="Yang, Yi" uniqKey="Yang Y" first="Yi" last="Yang">Yi Yang</name></author><author><name sortKey="Zhang, Chenggang" sort="Zhang, Chenggang" uniqKey="Zhang C" first="Chenggang" last="Zhang">Chenggang Zhang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="doi">10.1093/bioinformatics/btr582</idno><idno type="RBID">pubmed:22016409</idno><idno type="pmid">22016409</idno><idno type="wicri:Area/PubMed/Corpus">000299</idno><idno 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Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing 100850</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Qu, Wubin" sort="Qu, Wubin" uniqKey="Qu W" first="Wubin" last="Qu">Wubin Qu</name></author><author><name sortKey="Lu, Yiming" sort="Lu, Yiming" uniqKey="Lu Y" first="Yiming" last="Lu">Yiming Lu</name></author><author><name sortKey="Zhang, Yanchun" sort="Zhang, Yanchun" uniqKey="Zhang Y" first="Yanchun" last="Zhang">Yanchun Zhang</name></author><author><name sortKey="Wang, Xiaolei" sort="Wang, Xiaolei" uniqKey="Wang X" first="Xiaolei" last="Wang">Xiaolei Wang</name></author><author><name sortKey="Zhao, Dongsheng" sort="Zhao, Dongsheng" uniqKey="Zhao D" first="Dongsheng" last="Zhao">Dongsheng Zhao</name></author><author><name sortKey="Yang, Yi" sort="Yang, Yi" uniqKey="Yang Y" first="Yi" last="Yang">Yi Yang</name></author><author><name sortKey="Zhang, Chenggang" sort="Zhang, Chenggang" uniqKey="Zhang C" first="Chenggang" last="Zhang">Chenggang Zhang</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="e-ISSN">1367-4811</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>DNA Primers (genetics)</term><term>Exons</term><term>Humans</term><term>Membrane Proteins (genetics)</term><term>Mice</term><term>Nerve Tissue Proteins (genetics)</term><term>Open Reading Frames</term><term>Polymerase Chain Reaction</term><term>Polymorphism, Single Nucleotide</term><term>Protein Isoforms (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Primers</term><term>Membrane Proteins</term><term>Nerve Tissue Proteins</term><term>Protein Isoforms</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Exons</term><term>Humans</term><term>Mice</term><term>Open Reading Frames</term><term>Polymerase Chain Reaction</term><term>Polymorphism, Single Nucleotide</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><noCountry><name sortKey="Lu, Yiming" sort="Lu, Yiming" uniqKey="Lu Y" first="Yiming" last="Lu">Yiming Lu</name><name sortKey="Qu, Wubin" sort="Qu, Wubin" uniqKey="Qu W" first="Wubin" last="Qu">Wubin Qu</name><name sortKey="Wang, Xiaolei" sort="Wang, Xiaolei" uniqKey="Wang X" first="Xiaolei" last="Wang">Xiaolei Wang</name><name sortKey="Yang, Yi" sort="Yang, Yi" uniqKey="Yang Y" first="Yi" last="Yang">Yi Yang</name><name sortKey="Zhang, Chenggang" sort="Zhang, Chenggang" uniqKey="Zhang C" first="Chenggang" last="Zhang">Chenggang Zhang</name><name sortKey="Zhang, Yanchun" sort="Zhang, Yanchun" uniqKey="Zhang Y" first="Yanchun" last="Zhang">Yanchun Zhang</name><name sortKey="Zhao, Dongsheng" sort="Zhao, Dongsheng" uniqKey="Zhao D" first="Dongsheng" last="Zhao">Dongsheng Zhao</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Zhou, Yang" sort="Zhou, Yang" uniqKey="Zhou Y" first="Yang" last="Zhou">Yang Zhou</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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