메뉴 건너뛰기




Volumn , Issue , 2011, Pages 345-351

PRIMEGENSw3: A web-based tool for high-throughput primer and probe design

Author keywords

bisulfite sequencing; crosshybridization; PCR primer; PRIMEGENS; primer design; probe

Indexed keywords

BISULFITE-SEQUENCING; CROSS-HYBRIDIZATION; PCR PRIMERS; PRIMEGENS; PRIMER-DESIGN;

EID: 84863396828     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2011.43     Document Type: Conference Paper
Times cited : (2)

References (43)
  • 1
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Clifton, N.J.
    • Rozen, S. and Skaletsky, H. Primer3 on the WWW for general users and for biologist programmers. Methods in molecular biology (Clifton, N.J.), 2000, 132, 365-386.
    • (2000) Methods in Molecular Biology , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 3
    • 0032526879 scopus 로고    scopus 로고
    • Primer design for large scale sequencing
    • DOI 10.1093/nar/26.12.3006
    • Haas, S., Vingron, M., Poustka, A. and Wiemann, S. Primer design for large scale sequencing. Nucleic acids research, 1998, 26, 3006-3012. (Pubitemid 28297537)
    • (1998) Nucleic Acids Research , vol.26 , Issue.12 , pp. 3006-3012
    • Haas, S.1    Vingron, M.2    Poustka, A.3    Wiemann, S.4
  • 4
    • 0029855834 scopus 로고    scopus 로고
    • Primer Master: A new program for the design and analysis of PCR primers
    • Proutski, V. and Holmes, E.C. Primer Master: a new program for the design and analysis of PCR primers. Computer applications in the biosciences : CABIOS, 1996, 12, 253-255. (Pubitemid 26355602)
    • (1996) Computer Applications in the Biosciences , vol.12 , Issue.3 , pp. 253-255
    • Proutski, V.1    Holmes, E.C.2
  • 5
    • 0031569391 scopus 로고    scopus 로고
    • PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing
    • DOI 10.1006/geno.1996.4560
    • Li, P., Kupfer, K.C., Davies, C.J., Burbee, D., Evans, G.A. and Garner, H.R. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics, 1997, 40, 476-485. (Pubitemid 27137001)
    • (1997) Genomics , vol.40 , Issue.3 , pp. 476-485
    • Li, P.1    Kupfer, K.C.2    Davies, C.J.3    Burbee, D.4    Evans, G.A.5    Garner, H.R.6
  • 7
    • 33747822327 scopus 로고    scopus 로고
    • PrimerStation: A highly specific multiplex genomic PCR primer design server for the human genome
    • DOI 10.1093/nar/gkl297
    • Yamada, T., Soma, H. and Morishita, S. PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome. Nucleic acids research, 2006, 34, W665-669. (Pubitemid 44529854)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Yamada, T.1    Soma, H.2    Morishita, S.3
  • 9
    • 7244257594 scopus 로고    scopus 로고
    • PerlPrimer: Cross-platform, graphical primer design for standard, bisulphite and real-time PCR
    • DOI 10.1093/bioinformatics/bth254
    • Marshall, O.J. PerlPrimer: crossplatform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics (Oxford, England), 2004, 20, 2471-2472. (Pubitemid 39429922)
    • (2004) Bioinformatics , vol.20 , Issue.15 , pp. 2471-2472
    • Marshall, O.J.1
  • 10
    • 19744383664 scopus 로고    scopus 로고
    • BiSearch: Primer-design and search tool for PCR on bisulfite-treated genomes
    • Tusnady, G.E., Simon, I., Varadi, A. and Aranyi, T. BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes. Nucleic acids research, 2005, 33, e9.
    • (2005) Nucleic Acids Research , vol.33
    • Tusnady, G.E.1    Simon, I.2    Varadi, A.3    Aranyi, T.4
  • 11
    • 36049043696 scopus 로고    scopus 로고
    • BiSearch: ePCR tool for native or bisulfite-treated genomic template
    • DOI 10.1385/1-59745-528-8:385, PCR Primer Design
    • Aranyi, T. and Tusnady, G.E. BiSearch:ePCR tool for native or bisulfite-treated genomic template. Methods in molecular biology (Clifton, N.J.), 2007, 402, 385-402. (Pubitemid 350190099)
    • (2007) Methods in Molecular Biology , vol.402 , pp. 385-402
    • Aranyi, T.1    Tusnady, G.E.2
  • 14
    • 58149307466 scopus 로고    scopus 로고
    • QuantPrime - A flexible tool for reliable high-throughput primer design for quantitative PCR
    • Arvidsson, S., Kwasniewski, M., Riano-Pachon, D.M. and Mueller-Roeber, B. QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC bioinformatics, 2008, 9, 465.
    • (2008) BMC Bioinformatics , vol.9 , pp. 465
    • Arvidsson, S.1    Kwasniewski, M.2    Riano-Pachon, D.M.3    Mueller-Roeber, B.4
  • 15
    • 1842844023 scopus 로고    scopus 로고
    • PRIMEGENS: Robust and efficient design of gene-specific probes for microarray analysis
    • Xu, D., Li, G., Wu, L., Zhou, J. and Xu, Y. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics (Oxford, England), 2002, 18, 1432-1437. (Pubitemid 35414533)
    • (2002) Bioinformatics , vol.18 , Issue.11 , pp. 1432-1437
    • Xu, D.1    Li, G.2    Wu, L.3    Zhou, J.4    Xu, Y.5
  • 17
    • 50549102884 scopus 로고    scopus 로고
    • PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands
    • Srivastava, G.P., Guo, J., Shi, H. and Xu, D. PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics (Oxford, England), 2008, 24, 1837-1842.
    • (2008) Bioinformatics (Oxford, England) , vol.24 , pp. 1837-1842
    • Srivastava, G.P.1    Guo, J.2    Shi, H.3    Xu, D.4
  • 20
    • 84863414221 scopus 로고    scopus 로고
    • High-throughput Primer and Probe Design for Genome-Wide DNA Methylation Study Using PRIMEGENS
    • iConcept Press Ltd.
    • Srivastava, G.P., Kushwaha, G., Shi, H. and Xu, D. High-throughput Primer and Probe Design for Genome-Wide DNA Methylation Study Using PRIMEGENS. In "A Practical Guide to Bioinformatics Analysis". iConcept Press Ltd. 151-171, 2010.
    • (2010) A Practical Guide to Bioinformatics Analysis , pp. 151-171
    • Srivastava, G.P.1    Kushwaha, G.2    Shi, H.3    Xu, D.4
  • 22
    • 0002263171 scopus 로고
    • Theory of the melting transition of synthetic polynucleotides: Evaluation of the stacking free energy
    • Crothers, D.M. and Zimm, B.H. Theory of the melting transition of synthetic polynucleotides: evaluation of the stacking free energy. J. Mol. Biol. 1964, 9, 1-9.
    • (1964) J. Mol. Biol. , vol.9 , pp. 1-9
    • Crothers, D.M.1    Zimm, B.H.2
  • 23
    • 0000140192 scopus 로고
    • The stability of helical polynucleotides: Base contributions
    • DeVoe, H. and Tinoco, I., Jr. The stability of helical polynucleotides: base contributions. J. Mol. Biol. 1962, 4, 500-517.
    • (1962) J. Mol. Biol. , vol.4 , pp. 500-517
    • DeVoe, H.1    Tinoco Jr., I.2
  • 24
    • 84982401389 scopus 로고
    • A new approach to the study of sequence-dependent properties of polynucleotides
    • Gray, D.M. and Tinoco, I., Jr. A new approach to the study of sequence-dependent properties of polynucleotides. Biopolymers, 1970, 9, 223-244.
    • (1970) Biopolymers , vol.9 , pp. 223-244
    • Gray, D.M.1    Tinoco Jr., I.2
  • 29
    • 0025037431 scopus 로고
    • Optimization of the annealing temperature for DNA amplification in vitro
    • Rychlik, W., Spencer, W.J., Rhoads, R.E. Optimization of the annealing temperature for DNA amplification in vitro.Nucleic Acids Res. 1990, 18 (21), 6409-6412.
    • (1990) Nucleic Acids Res. , vol.18 , Issue.21 , pp. 6409-6412
    • Rychlik, W.1    Spencer, W.J.2    Rhoads, R.E.3
  • 30
    • 0031432735 scopus 로고    scopus 로고
    • Predicting sequence-dependent melting stability of short duplex DNA oligomers
    • Owczarzy, R., Vallone, P.M., Gallo, F.J., Paner, T.M., Lane, M.J. and Benight, A.S. Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers, 1997, 44 (3), 217-239.
    • (1997) Biopolymers , vol.44 , Issue.3 , pp. 217-239
    • Owczarzy, R.1    Vallone, P.M.2    Gallo, F.J.3    Paner, T.M.4    Lane, M.J.5    Benight, A.S.6
  • 31
    • 0027442905 scopus 로고
    • Influence of nearest neighbor sequence on the stability of base pair mismatches in long DNA: Determination by temperature-gradient gel electrophoresis
    • Ke, S-H. and Wartell, R.M. Influence of nearest neighbor sequence on the stability of base pair mismatches in long DNA: determination bytemperature-gradient gel electrophoresis. Nucleic Acids Research, 1993, 21(22) 5137-5143 (Pubitemid 23342524)
    • (1993) Nucleic Acids Research , vol.21 , Issue.22 , pp. 5137-5143
    • Ke, S.-H.1    Wartell, R.M.2
  • 32
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • DOI 10.1021/bi951907q
    • SantaLucia J., Jr., Allawi H.T., and Seneviratne P.A. Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability. Biochemistry 1996, 35, 3555-3562 (Pubitemid 26092574)
    • (1996) Biochemistry , vol.35 , Issue.11 , pp. 3555-3562
    • SantaLucia Jr., J.1    Allawi, H.T.2    Seneviratne, P.A.3
  • 33
    • 0032539693 scopus 로고    scopus 로고
    • Unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • Santalucia J.A. unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamicsProc. Natl. Acad. Sci., 1998, 95, 1460-1465.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 1460-1465
    • Santalucia, J.A.1
  • 34
    • 0033596964 scopus 로고    scopus 로고
    • Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal AA, CC, GG, and TT Mismatches
    • Peyret, N., Seneviratne, P.A., Allawi, H.T., and SantaLucia, J. Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal AA, CC, GG, and TT Mismatches Biochemistry, 1999, 38, 3468-3477.
    • (1999) Biochemistry , vol.38 , pp. 3468-3477
    • Peyret, N.1    Seneviratne, P.A.2    Allawi, H.T.3    SantaLucia, J.4
  • 35
    • 0029949375 scopus 로고    scopus 로고
    • Software to determine optimal oligonucleotide sequences based on hybridization simulation data
    • Hyndman, D., Cooper, A., Pruzinsky, S., Coad, D. and Mitsuhashi, M. Software to determine optimal oligonucleotide sequences based on hybridization simulation data. BioTechniques, 1996, 20, 1090-1094, 1096-1097.
    • (1996) BioTechniques , vol.20
    • Hyndman, D.1    Cooper, A.2    Pruzinsky, S.3    Coad, D.4    Mitsuhashi, M.5
  • 36
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal G•T mismatches in DNA
    • DOI 10.1021/bi962590c
    • Allawi, H.T., and SantaLucia, J., Jr. Thermodynamics and NMR of Internal G•T Mismatches in DNA. Biochemistry, 1997, 36, 10581-10594. (Pubitemid 27374152)
    • (1997) Biochemistry , vol.36 , Issue.34 , pp. 10581-10594
    • Allawi, H.T.1    Santalucia Jr., J.2
  • 37
    • 0032581024 scopus 로고    scopus 로고
    • Nearest-Neighbor Thermodynamics of Internal A•C Mismatches in DNA: Sequence Dependence and pH Effects
    • Allawi, H.T., and SantaLucia, J., Jr. Nearest-Neighbor Thermodynamics of Internal A•C Mismatches in DNA: Sequence Dependence and pH Effects Biochemistry, 1998, 37, 9435-9444.
    • (1998) Biochemistry , vol.37 , pp. 9435-9444
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 38
    • 0032102940 scopus 로고    scopus 로고
    • Thermodynamics of internal C•T mismatches in DNA
    • Allawi, H.T., and SantaLucia, J., Jr. Thermodynamics of internal C•T mismatches in DNA Nucleic Acids Res., 1998, 26, 2694-2701.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2694-2701
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 39
    • 0032562140 scopus 로고    scopus 로고
    • Nearest neighbor thermodynamic parameters for internal G•A mismatches in DNA
    • DOI 10.1021/bi9724873
    • Allawi, H.T., and SantaLucia, J., Jr. Nearest Neighbor Thermodynamic Parameters for Internal G•A Mismatches in DNA. Biochemistry, 1998, 37, 2170-2179. (Pubitemid 28119290)
    • (1998) Biochemistry , vol.37 , Issue.8 , pp. 2170-2179
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 40
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in caenorhabditis elegans
    • DOI 10.1038/35888
    • Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 1998, 391, 806-811. (Pubitemid 28099681)
    • (1998) Nature , vol.391 , Issue.6669 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.K.3    Kostas, S.A.4    Driver, S.E.5    Mello, C.C.6
  • 42
    • 33846545543 scopus 로고    scopus 로고
    • Molecular biology. Amplified silencing
    • Baulcombe, D.C. Molecular biology. Amplified silencing. Science, 2007, 315, 199-200.
    • (2007) Science , vol.315 , pp. 199-200
    • Baulcombe, D.C.1
  • 43
    • 78049263858 scopus 로고    scopus 로고
    • MiRNAs in the biogenesis of transacting siRNAs in higher plants
    • Allen, E., Howell, M.D. miRNAs in the biogenesis of transacting siRNAs in higher plants. Semin Cell Dev Biol. 2010, 8, 798-804.
    • (2010) Semin Cell Dev Biol. , vol.8 , pp. 798-804
    • Allen, E.1    Howell, M.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.