RTPrimerDB: the portal for real-time PCR primers and probes

被引：120

作者：

Lefever, Steve ^{[1
]}

Vandesompele, Jo ^{[1
]}

Speleman, Frank ^{[1
]}

Pattyn, Filip ^{[1
]}

机构：

[1] Ghent Univ Hosp, Ctr Med Genet, B-9000 Ghent, Belgium

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

关键词：

DATABASE; SOFTWARE; UPDATE; NCBI;

D O I：

10.1093/nar/gkn777

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

RTPrimerDB (http://www.rtprimerdb.org) is a freely accessible database and analysis tool for real-time quantitative PCR assays. RTPrimerDB includes records with user submitted assays that are linked to genome information from reference databases and quality controlled using an in silico assay evaluation system. The primer evaluation tools intended to assess the specificity and to detect features that could negatively affect the amplification efficiency are combined into a pipeline to test custom-designed primer and probe sequences. An improved user feedback system guides users and submitters to enter practical remarks and details about experimental evaluation analyses. The database is linked with reference databases to allow the submission of assays for all genes and organisms officially registered in Entrez Gene and RefSeq. Records in RTPrimerDB are assigned unique and stable identifiers. The content is provided via an interactive web-based search system and is available for download in the recently developed RDML format and as bulk export file. RTPrimerDB is a one-stop portal for high-quality and highly annotated real-time PCR assays.

引用

页码：D942 / D945

页数：4

共 10 条

[1]

Aranyi Tamas, 2007, V402, P385

[2] Ensembl 2008 [J].

Flicek, P. ;

Aken, B. L. ;

Beal, K. ;

Ballester, B. ;

Caccamo, M. ;

Chen, Y. ;

Clarke, L. ;

Coates, G. ;

Cunningham, F. ;

Cutts, T. ;

Down, T. ;

Dyer, S. C. ;

Eyre, T. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Holland, R. ;

Howe, K. L. ;

Howe, K. ;

Johnson, N. ;

Jenkinson, A. ;

Kahari, A. ;

Keefe, D. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Pritchard, B. ;

Prlic, A. ;

Rice, S. ;

Rios, D. ;

Schuster, M. ;

Sealy, I. ;

Slater, G. ;

Smedley, D. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. J. ;

Vogel, J. ;

White, S. ;

Wood, M. ;

Birney, E. ;

Cox, T. ;

Curwen, V. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D707-D714

[3] qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data [J].

Hellemans, Jan ;

Mortier, Geert ;

De Paepe, Anne ;

Speleman, Frank ;

Vandesompele, Jo .

GENOME BIOLOGY, 2007, 8 (02)

[4] The UCSC Genome Browser Database: 2008 update [J].

Karolchik, D. ;

Kuhn, R. M. ;

Baertsch, R. ;

Barber, G. P. ;

Clawson, H. ;

Diekhans, M. ;

Giardine, B. ;

Harte, R. A. ;

Hinrichs, A. S. ;

Hsu, F. ;

Kober, K. M. ;

Miller, W. ;

Pedersen, J. S. ;

Pohl, A. ;

Raney, B. J. ;

Rhead, B. ;

Rosenbloom, K. R. ;

Smith, K. E. ;

Stanke, M. ;

Thakkapallayil, A. ;

Trumbower, H. ;

Wang, T. ;

Zweig, A. S. ;

Haussler, D. ;

Kent, W. J. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D773-D779

[5] Entrez Gene: gene-centered information at NCBI [J].

Maglott, Donna ;

Ostell, Jim ;

Pruitt, Kim D. ;

Tatusova, Tatiana .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D26-D31

[6]

Markham Nicholas R., 2008, V453, P3, DOI 10.1007/978-1-60327-429-6_1

[7] RTPrimerDB: The Real-Time PCR primer and probe database [J].

Pattyn, F ;

Speleman, F ;

De Paepe, A ;

Vandesompele, J .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :122-123

[8] RTPrimerDB: the real-time PCR primer and probe database, major update 2006 [J].

Pattyn, Filip ;

Robbrecht, Piet ;

De Paepe, Anne ;

Speleman, Frank ;

Vandesompele, Jo .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D684-D688

[9] NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins [J].

Pruitt, Kim D. ;

Tatusova, Tatiana ;

Maglott, Donna R. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D61-D65

[10] Promoting coherent minimum reporting guidelines for biological and biomedical investigations:: the MIBBI project [J].

Taylor, Chris F. ;

Field, Dawn ;

Sansone, Susanna-Assunta ;

Aerts, Jan ;

Apweiler, Rolf ;

Ashburner, Michael ;

Ball, Catherine A. ;

Binz, Pierre-Alain ;

Bogue, Molly ;

Booth, Tim ;

Brazma, Alvis ;

Brinkman, Ryan R. ;

Clark, Adam Michael ;

Deutsch, Eric W. ;

Fiehn, Oliver ;

Fostel, Jennifer ;

Ghazal, Peter ;

Gibson, Frank ;

Gray, Tanya ;

Grimes, Graeme ;

Hancock, John M. ;

Hardy, Nigel W. ;

Hermjakob, Henning ;

Julian, Randall K., Jr. ;

Kane, Matthew ;

Kettner, Carsten ;

Kinsinger, Christopher ;

Kolker, Eugene ;

Kuiper, Martin ;

Le Novere, Nicolas ;

Leebens-Mack, Jim ;

Lewis, Suzanna E. ;

Lord, Phillip ;

Mallon, Ann-Marie ;

Marthandan, Nishanth ;

Masuya, Hiroshi ;

McNally, Ruth ;

Mehrle, Alexander ;

Morrison, Norman ;

Orchard, Sandra ;

Quackenbush, John ;

Reecy, James M. ;

Robertson, Donald G. ;

Rocca-Serra, Philippe ;

Rodriguez, Henry ;

Rosenfelder, Heiko ;

Santoyo-Lopez, Javier ;

Scheuermann, Richard H. ;

Schober, Daniel ;

Smith, Barry .

NATURE BIOTECHNOLOGY, 2008, 26 (08) :889-896

← 1 →