RTPrimerDB: the real-time PCR primer and probe database, major update 2006
Identifieur interne : 001622 ( Main/Exploration ); précédent : 001621; suivant : 001623RTPrimerDB: the real-time PCR primer and probe database, major update 2006
Auteurs : Filip Pattyn [Belgique] ; Piet Robbrecht [Belgique] ; Anne De Paepe [Belgique] ; Frank Speleman [Belgique] ; Jo Vandesompele [Belgique]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2006-01.
Abstract
The RTPrimerDB (http://medgen.ugent.be/rtprimerdb) project provides a freely accessible data retrieval system and an in silico assay evaluation pipeline for real-time quantitative PCR assays. Over the last year the number of user submitted assays has grown to 3500. Data conveyance from Entrez Gene by establishing an assay-to-gene relationship enables the addition of new primer assays for one of the 1.5 million different genes from 2300 species stored in the system. Easy access to the primer and probe data is possible by using multiple search criteria. Assay reports contain gene information, assay details (such as oligonucleotide sequences, detection chemistry and reaction conditions), publication information, users' experimental evaluation feedback and submitter's contact details. Gene expression assays are extended with a scalable assay viewer that provides detailed information on the alignment of primer and probe sequences on the known transcript variants of a gene, along with Single Nucleotide Polymorphisms (SNP) positions and peptide domain information. Furthermore, an mfold module is implemented to predict the secondary structure of the amplicon sequence, as this has been reported to impact the efficiency of the PCR. RTPrimerDB is also extended with an in silico analysis pipeline to streamline the evaluation of custom designed primer and probe sequences prior to ordering and experimental evaluation. In a secured environment, the pipeline performs automated BLAST specificity searches, mfold secondary structure prediction, SNP or plain sequence error identification, and graphical visualization of the aligned primer and probe sequences on the target gene.
Url:
DOI: 10.1093/nar/gkj155
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000255
- to stream Istex, to step Curation: 000255
- to stream Istex, to step Checkpoint: 001068
- to stream Main, to step Merge: 001630
- to stream Main, to step Curation: 001622
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">RTPrimerDB: the real-time PCR primer and probe database, major update 2006</title><author><name sortKey="Pattyn, Filip" sort="Pattyn, Filip" uniqKey="Pattyn F" first="Filip" last="Pattyn">Filip Pattyn</name></author><author><name sortKey="Robbrecht, Piet" sort="Robbrecht, Piet" uniqKey="Robbrecht P" first="Piet" last="Robbrecht">Piet Robbrecht</name></author><author><name sortKey="De Paepe, Anne" sort="De Paepe, Anne" uniqKey="De Paepe A" first="Anne" last="De Paepe">Anne De Paepe</name></author><author><name sortKey="Speleman, Frank" sort="Speleman, Frank" uniqKey="Speleman F" first="Frank" last="Speleman">Frank Speleman</name></author><author><name sortKey="Vandesompele, Jo" sort="Vandesompele, Jo" uniqKey="Vandesompele J" first="Jo" last="Vandesompele">Jo Vandesompele</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:46D20F5A5EF148E5F61B221849E9FFC9B9BFE85B</idno><date when="2006" year="2006">2006</date><idno type="doi">10.1093/nar/gkj155</idno><idno type="url">https://api.istex.fr/document/46D20F5A5EF148E5F61B221849E9FFC9B9BFE85B/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000255</idno><idno type="wicri:Area/Istex/Curation">000255</idno><idno type="wicri:Area/Istex/Checkpoint">001068</idno><idno type="wicri:doubleKey">0305-1048:2006:Pattyn F:rtprimerdb:the:real</idno><idno type="wicri:Area/Main/Merge">001630</idno><idno type="wicri:Area/Main/Curation">001622</idno><idno type="wicri:Area/Main/Exploration">001622</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">RTPrimerDB: the real-time PCR primer and probe database, major update 2006</title><author><name sortKey="Pattyn, Filip" sort="Pattyn, Filip" uniqKey="Pattyn F" first="Filip" last="Pattyn">Filip Pattyn</name><affiliation wicri:level="3"><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Medical Genetics Ghent (CMGG), Ghent University Hospital De Pintelaan 185, 9000 Ghent</wicri:regionArea><placeName><region type="province" nuts="2">Province de Flandre-Orientale</region><settlement type="city">Gand</settlement></placeName></affiliation></author><author><name sortKey="Robbrecht, Piet" sort="Robbrecht, Piet" uniqKey="Robbrecht P" first="Piet" last="Robbrecht">Piet Robbrecht</name><affiliation wicri:level="3"><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Medical Genetics Ghent (CMGG), Ghent University Hospital De Pintelaan 185, 9000 Ghent</wicri:regionArea><placeName><region type="province" nuts="2">Province de Flandre-Orientale</region><settlement type="city">Gand</settlement></placeName></affiliation></author><author><name sortKey="De Paepe, Anne" sort="De Paepe, Anne" uniqKey="De Paepe A" first="Anne" last="De Paepe">Anne De Paepe</name><affiliation wicri:level="3"><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Medical Genetics Ghent (CMGG), Ghent University Hospital De Pintelaan 185, 9000 Ghent</wicri:regionArea><placeName><region type="province" nuts="2">Province de Flandre-Orientale</region><settlement type="city">Gand</settlement></placeName></affiliation></author><author><name sortKey="Speleman, Frank" sort="Speleman, Frank" uniqKey="Speleman F" first="Frank" last="Speleman">Frank Speleman</name><affiliation wicri:level="3"><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Medical Genetics Ghent (CMGG), Ghent University Hospital De Pintelaan 185, 9000 Ghent</wicri:regionArea><placeName><region type="province" nuts="2">Province de Flandre-Orientale</region><settlement type="city">Gand</settlement></placeName></affiliation></author><author><name sortKey="Vandesompele, Jo" sort="Vandesompele, Jo" uniqKey="Vandesompele J" first="Jo" last="Vandesompele">Jo Vandesompele</name><affiliation wicri:level="3"><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Medical Genetics Ghent (CMGG), Ghent University Hospital De Pintelaan 185, 9000 Ghent</wicri:regionArea><placeName><region type="province" nuts="2">Province de Flandre-Orientale</region><settlement type="city">Gand</settlement></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j">Nucleic Acids Research</title><title level="j" type="abbrev">Nucl. Acids Res.</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2006-01">2006-01</date><biblScope unit="volume">34</biblScope><biblScope unit="supplement">suppl_1</biblScope><biblScope unit="page" from="D684">D684</biblScope><biblScope unit="page" to="D688">D688</biblScope></imprint><idno type="ISSN">0305-1048</idno></series><idno type="istex">46D20F5A5EF148E5F61B221849E9FFC9B9BFE85B</idno><idno type="DOI">10.1093/nar/gkj155</idno><idno type="local">gkj155</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The RTPrimerDB (http://medgen.ugent.be/rtprimerdb) project provides a freely accessible data retrieval system and an in silico assay evaluation pipeline for real-time quantitative PCR assays. Over the last year the number of user submitted assays has grown to 3500. Data conveyance from Entrez Gene by establishing an assay-to-gene relationship enables the addition of new primer assays for one of the 1.5 million different genes from 2300 species stored in the system. Easy access to the primer and probe data is possible by using multiple search criteria. Assay reports contain gene information, assay details (such as oligonucleotide sequences, detection chemistry and reaction conditions), publication information, users' experimental evaluation feedback and submitter's contact details. Gene expression assays are extended with a scalable assay viewer that provides detailed information on the alignment of primer and probe sequences on the known transcript variants of a gene, along with Single Nucleotide Polymorphisms (SNP) positions and peptide domain information. Furthermore, an mfold module is implemented to predict the secondary structure of the amplicon sequence, as this has been reported to impact the efficiency of the PCR. RTPrimerDB is also extended with an in silico analysis pipeline to streamline the evaluation of custom designed primer and probe sequences prior to ordering and experimental evaluation. In a secured environment, the pipeline performs automated BLAST specificity searches, mfold secondary structure prediction, SNP or plain sequence error identification, and graphical visualization of the aligned primer and probe sequences on the target gene.</div></front></TEI><affiliations><list><country><li>Belgique</li></country><region><li>Province de Flandre-Orientale</li></region><settlement><li>Gand</li></settlement></list><tree><country name="Belgique"><region name="Province de Flandre-Orientale"><name sortKey="Pattyn, Filip" sort="Pattyn, Filip" uniqKey="Pattyn F" first="Filip" last="Pattyn">Filip Pattyn</name></region><name sortKey="De Paepe, Anne" sort="De Paepe, Anne" uniqKey="De Paepe A" first="Anne" last="De Paepe">Anne De Paepe</name><name sortKey="Robbrecht, Piet" sort="Robbrecht, Piet" uniqKey="Robbrecht P" first="Piet" last="Robbrecht">Piet Robbrecht</name><name sortKey="Speleman, Frank" sort="Speleman, Frank" uniqKey="Speleman F" first="Frank" last="Speleman">Frank Speleman</name><name sortKey="Vandesompele, Jo" sort="Vandesompele, Jo" uniqKey="Vandesompele J" first="Jo" last="Vandesompele">Jo Vandesompele</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Belgique/explor/OpenAccessBelV2/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001622 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001622 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Belgique
|area= OpenAccessBelV2
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:46D20F5A5EF148E5F61B221849E9FFC9B9BFE85B
|texte= RTPrimerDB: the real-time PCR primer and probe database, major update 2006
}}
| This area was generated with Dilib version V0.6.25. |  |