Primer3—new capabilities and interfaces

Nucleic Acids Research - Tập 40 Số 15 - Trang e115-e115 - 2012
Andreas Untergasser1, Ioana Cutcutache1, Triinu Kõressaar1, Jian Ye1, Brant C. Faircloth1, Maido Remm1, Steve Rozen1
1Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany, 2Neurobiology and Behavioral Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, 3Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia, 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 5Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA

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Tài liệu tham khảo

Plasterer, 1997, PRIMERSELECT. Primer and probe design, Methods Mol. Biol., 70, 291

Applied Biosystems, 2004, Primer Express® Software Version 3.0 Getting Started Guide

Rychlik, 2007, OLIGO 7 primer analysis software, Methods Mol. Biol., 402, 35, 10.1007/978-1-59745-528-2_2

Rychlik, 2010, OLIGO Primer Analysis Software Version 7

Rozen, 2000, Primer3 on the WWW for general users and for biologist programmers, Bioinformatics Methods and Protocols, 365

SantaLucia, 2007, Physical principles and visual-OMP software for optimal PCR design, Methods Mol. Biol., 402, 3, 10.1007/978-1-59745-528-2_1

Srivastava, 2007, Genome-scale probe and primer design with PRIMEGENS, Methods Mol. Biol., 402, 159, 10.1007/978-1-59745-528-2_8

Srivastava, 2008, PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands, Bioinformatics, 24, 1837, 10.1093/bioinformatics/btn320

Srivastava, 2011, Homolog-specific PCR primer design for profiling splice variants, Nucleic Acids Res., 39, e69, 10.1093/nar/gkr127

van Baren, 2004, The PCR suite, Bioinformatics, 20, 591, 10.1093/bioinformatics/btg473

Sayers, 2012, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., 40, D13, 10.1093/nar/gkr1184

You, 2008, BatchPrimer3: a high throughput web application for PCR and sequencing primer design, BMC Bioinformatics, 9, 253, 10.1186/1471-2105-9-253

Allawi, 1997, Thermodynamics and NMR of internal G.T mismatches in DNA, Biochemistry, 36, 10581, 10.1021/bi962590c

Allawi, 1998, Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects, Biochemistry, 37, 9435, 10.1021/bi9803729

Allawi, 1998, Thermodynamics of internal C.T mismatches in DNA, Nucleic Acids Res., 26, 2694, 10.1093/nar/26.11.2694

Allawi, 1998, Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA, Biochemistry, 37, 2170, 10.1021/bi9724873

Bommarito, 2000, Thermodynamic parameters for DNA sequences with dangling ends, Nucleic Acids Res., 28, 1929, 10.1093/nar/28.9.1929

Peyret, 1999, Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches, Biochemistry, 38, 3468, 10.1021/bi9825091

SantaLucia, 1998, A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proc. Natl Acad. Sci. USA., 95, 1460, 10.1073/pnas.95.4.1460

SantaLucia, 2004, The thermodynamics of DNA structural motifs, Annu. Rev. Biophys. Biomol. Struct., 33, 415, 10.1146/annurev.biophys.32.110601.141800

Andreson, 2006, GENOMEMASKER package for designing unique genomic PCR primers, BMC Bioinformatics, 7, 172, 10.1186/1471-2105-7-172

Untergasser, 2007, Primer3Plus, an enhanced web interface to Primer3, Nucleic Acids Res., 35, W71, 10.1093/nar/gkm306

Land, 1960, An automatic method of solving discrete programming problems, Econometrica, 28, 497, 10.2307/1910129

Genome 10K Community of Scientists, 2009, Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species, J. Hered., 100, 659, 10.1093/jhered/esp086

Lefever, 2009, RDML: structured language and reporting guidelines for real-time quantitative PCR data, Nucleic Acids Res., 37, 2065, 10.1093/nar/gkp056

McKay, 2002, AcePrimer: automation of PCR primer design based on gene structure, Bioinformatics, 18, 1538, 10.1093/bioinformatics/18.11.1538

Wrobel, 2004, AutoPrime: selecting primers for expressed sequences, Genome Biol., 5, P11, 10.1186/gb-2004-5-5-p11

You, 2009, ConservedPrimers 2.0: a high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery, BMC Bioinformatics, 10, 331, 10.1186/1471-2105-10-331

Wu, 2006, EasyExonPrimer: automated primer design for exon sequences, Appl. Bioinformatics, 5, 119, 10.2165/00822942-200605020-00007

Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25

Shen, 2010, MPprimer: a program for reliable multiplex PCR primer design, BMC Bioinformatics, 11, 143, 10.1186/1471-2105-11-143

Li, 2002, MethPrimer: designing primers for methylation PCRs, Bioinformatics, 18, 1427, 10.1093/bioinformatics/18.11.1427

Faircloth, 2008, msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design, Mol. Ecol. Resour., 8, 92, 10.1111/j.1471-8286.2007.01884.x

Koressaar, 2009, Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms, Bioinformatics, 25, 1349, 10.1093/bioinformatics/btp241

Brown, 2010, Optimus primer: a PCR enrichment primer design program for next-generation sequencing of human exonic regions, BMC Res. Notes, 3, 185, 10.1186/1756-0500-3-185

Gadberry, 2005, Primaclade–a flexible tool to find conserved PCR primers across multiple species, Bioinformatics, 21, 1263, 10.1093/bioinformatics/bti134

Xu, 2002, PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis, Bioinformatics, 18, 1432, 10.1093/bioinformatics/18.11.1432

Pessoa, 2010, PrimerIdent: a web based tool for conserved primer design, Bioinformation, 5, 52, 10.6026/97320630005052

Tsai, 2007, PrimerZ: streamlined primer design for promoters, exons and human SNPs, Nucleic Acids Res., 35, W63, 10.1093/nar/gkm383

Meglecz, 2010, QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects, Bioinformatics, 26, 403, 10.1093/bioinformatics/btp670

Kim, 2007, QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments, Bioinformatics, 23, 2331, 10.1093/bioinformatics/btm343

Arvidsson, 2008, QuantPrime–a flexible tool for reliable high-throughput primer design for quantitative PCR, BMC Bioinformatics, 9, 465, 10.1186/1471-2105-9-465

Piriyapongsa, 2009, RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation, BMC Genomics, 10, S4, 10.1186/1471-2164-10-S3-S4

Zhang, 2005, SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design, Nucleic Acids Res., 33, W489, 10.1093/nar/gki358

Weckx, 2007, SNPbox: web-based high-throughput primer design with an eye for repetitive sequences, Methods Mol. Biol., 402, 179

Weckx, 2005, SNPbox: a modular software package for large-scale primer design, Bioinformatics, 21, 385, 10.1093/bioinformatics/bti006

Andreson, 2006, SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes, Nucleic Acids Res., 34, W651, 10.1093/nar/gkl125

Vijaya Satya, 2010, A high-throughput pipeline for the design of real-time PCR signatures, BMC Bioinformatics, 11, 340, 10.1186/1471-2105-11-340

Martins, 2009, WebSat–a web software for microsatellite marker development, Bioinformation, 3, 282, 10.6026/97320630003282