Mixture models for analysis of melting temperature data

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Nellåker, Christoffer ^a   Uhrzander, Fredrik ^b   Tyrcha, Joanna ^b   Karlsson, Håkan ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AKAIKE'S INFORMATION CRITERIONS; HIGH RESOLUTION; MIXING PROPORTIONS; MIXTURE MODEL; MODEL CONSTRUCTION; REAL-TIME PCR; RELATIVE FREQUENCIES; TARGET SEQUENCES;

MELTING POINT; MIXTURES; POLYMERASE CHAIN REACTION;

COMPUTER SIMULATION;

AMPLICON; ARTICLE; BAYES THEOREM; MELTING POINT; METHODOLOGY; MOLECULAR MODEL; PLASMID; REAL TIME POLYMERASE CHAIN REACTION; SIMULATION; TEMPERATURE MEASUREMENT; ALGORITHM; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; DNA SEQUENCE; GENETICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICAL MODEL; TRANSITION TEMPERATURE;

DNA;

ALGORITHMS; COMPUTER SIMULATION; DNA; MODELS, CHEMICAL; MODELS, STATISTICAL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TRANSITION TEMPERATURE;

EID: 54049121802     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-370     Document Type: Article

References (20)

1. Germer S Higuchi R Single-tube genotyping without oligonucleotide probes Genome Res 1999, 9(1):72-78. 310703 9927486
2. Graziano C Giorgi M Malentacchi C Mattiuz PL Porfirio B Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes BMC Med Genet 2005, 6:36. 1260020 16202172 10.1186/1471-2350-6-36
3. Pham HM Konnai S Usui T Chang KS Murata S Mase M Ohashi K Onuma M Rapid detection and differentiation of Newcastle disease virus by real-time PCR with melting-curve analysis Arch Virol 2005, 150(12):2429-2438. 10.1007/s00705-005-0603-0 16052279
4. Waku-Kouomou D Alla A Blanquier B Jeantet D Caidi H Rguig A Freymuth F Wild FT Genotyping measles virus by real-time amplification refractory mutation system PCR represents a rapid approach for measles outbreak investigations J Clin Microbiol 2006, 44(2):487-494. 1392642 16455903 10.1128/JCM.44.2.487-494.2006
5. Harasawa R Mizusawa H Fujii M Yamamoto J Mukai H Uemori T Asada K Kato I Rapid detection and differentiation of the major Mycoplasma contaminants in cell cultures using real-time PCR with SYBR Green I and melting curve analysis Microbiol Immunol 2005, 49(9):859-863. 16172541
6. Nellåker C Yao Y Jones-Brando L Mallet F Yolken RH Karlsson H Transactivation of elements in the human endogenous retrovirus W family by viral infection Retrovirology 2006, 3(1):44. 1539011 16822326 10.1186/ 1742-4690-3-44
7. Yao Y Schröder J Nellåker C Bottmer C Bachmann S Yolken RH Karlsson H Elevated levels of human endogenous retrovirus-W transcripts in blood cells from patients with first episode schizophrenia Genes Brain Behav 2007, 7:103-112. 17559415
8. Nellåker C Wallgren U Karlsson H Molecular beacon-based temperature control and automated analyses for improved resolution of melting temperature analysis using SYBR I Green chemistry Clin Chem 2007, 53(1):98-103. 10.1373/clinchem.2006.075184 17110472
9. Volker J Blake RD Delcourt SG Breslauer KJ High-resolution calorimetric and optical melting profiles of DNA plasmids: Resolving contributions from intrinsic melting domains and specifically designed inserts Biopolymers 1999, 50(3):303-318. 10.1002/ (SICI)1097-0282(199909)50:3<303::AID-BIP6>3.0.CO;2-U 10397791
10. Wittwer CT Reed GH Gundry CN Vandersteen JG Pryor RJ High-resolution genotyping by amplicon melting analysis using LCGreen Clin Chem 2003, 49(6 Pt 1):853-860. 10.1373/49.6.853 12765979
11. Gundry CN Dobrowolski SF Martin YR Robbins TC Nay LM Boyd N Coyne T Wall MD Wittwer CT Teng DH Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons Nucleic Acids Res 2008, 36(10):3401-3408. 2425497 18448472 10.1093/nar/gkn204
12. Slinger R Bellfoy D Desjardins M Chan F High-resolution melting assay for the detection of gyrA mutations causing quinolone resistance in Salmonella enterica serovars Typhi and Paratyphi Diagn Microbiol Infect Dis 2007, 57(4):455-458. 10.1016/j.diagmicrobio.2006.09.011 17156963
13. Dempster AP Laird NM Rubin DB Maximum likelihood from incomplete data via the EM algorithm J Roy Statist Soc B 1977, 39(1):1-38.
14. McLachlan GJ Krishnan T The EM Algorithm and Extensions New York: Wiley 1997.
15. Dennis JJE Schnabel RB Numerical Methods for Unconstrained Optimization and Nonlinear Equations New Jersey: Prentice Hall 1983.
16. Akaike H A new look at the statistical model identification IEEE Trans Automat Control 1974, 19(6):716-723. 10.1109/TAC.1974.1100705
17. Akaike H (ed.) Information Theory and an Extension of the Maximum Likelihood Principle Budapest: Akademiai Kiado 1973.
18. Team RDC R: A Language and Environment for Statistical Computing Vienna, Austria: R Foundation for Statistical Computing 2.6.0 2008.
19. Macdonald P MIX Software for Mixture Distributions Ontario, Canada: Ichthus Data Systems 2.3, 1988.
20. Du J Combined algorithms for fitting finite mixture distributions Masters thesis Hamilton, Ontario: McMaster University 2002.