Electrophoretic trace simulator

Details Electrophoretic trace simulator Electrophoretic trace simulator

2007-05-22

2007-05-22

Phan, Thai (Department: 2128)

Data processing: structural design, modeling, simulation, and em

Modeling by mathematical expression

C703S012000, C435S006120

Reexamination Certificate

active

10295964

ABSTRACT:
A simulated electrophoretic trace is prepared by first obtaining an input file containing an input base sequence comprising a string of letters (A, C, G and/or T) in an order corresponding to the input base sequence, and then modifying the input file using one or more functions to take into account perturbations associated with (1) changes in peak intensity as a function of base number; (2) peak shape as a function of base number; (3) peak skew; (4) spacing between peaks; (5) background; (6) noise; (7) spectral cross-talk; (8) instrumental effects and/or (9) gel electrophoresis effects to produce a modified file representing a simulated electrophoretic trace. The method may be performed using a specially adapted apparatus.

REFERENCES:
patent: 3742202 (1973-06-01), Spreitzhofer
patent: 4329591 (1982-05-01), Fujiwara et al.
patent: 4363705 (1982-12-01), Hunyar et al.
patent: 4683194 (1987-07-01), Saiki et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis et al.
patent: 4720786 (1988-01-01), Hara
patent: 4729947 (1988-03-01), Middendorf et al.
patent: 4795699 (1989-01-01), Tabor et al.
patent: 4800159 (1989-01-01), Mullis et al.
patent: 4811218 (1989-03-01), Hunkapiller et al.
patent: 4823007 (1989-04-01), Hanson
patent: 4849513 (1989-07-01), Smith et al.
patent: 4855225 (1989-08-01), Fung et al.
patent: 4865968 (1989-09-01), Orgel et al.
patent: 4889818 (1989-12-01), Gelfand et al.
patent: 4941092 (1990-07-01), Hara et al.
patent: 4942124 (1990-07-01), Church
patent: 4960999 (1990-10-01), McKean et al.
patent: 4965188 (1990-10-01), Mullis et al.
patent: 4982326 (1991-01-01), Kaneko
patent: 5008182 (1991-04-01), Sninsky et al.
patent: 5075216 (1991-12-01), Innis et al.
patent: 5079352 (1992-01-01), Gelfand et al.
patent: 5096557 (1992-03-01), Simons
patent: 5108179 (1992-04-01), Myers
patent: 5118800 (1992-06-01), Smith et al.
patent: 5119316 (1992-06-01), Dam et al.
patent: 5122345 (1992-06-01), Tabor et al.
patent: 5124247 (1992-06-01), Ansorge
patent: 5171534 (1992-12-01), Smith et al.
patent: 5175082 (1992-12-01), Jeffreys
patent: 5176995 (1993-01-01), Sninsky et al.
patent: 5190632 (1993-03-01), Fujimiya et al.
patent: 5207880 (1993-05-01), Middendorf et al.
patent: 5213673 (1993-05-01), Fujimiya et al.
patent: 5246866 (1993-09-01), Nasu et al.
patent: 5268486 (1993-12-01), Waggoner et al.
patent: 5273632 (1993-12-01), Stockham et al.
patent: 5283171 (1994-02-01), Manos et al.
patent: 5290419 (1994-03-01), Kambara et al.
patent: 5308751 (1994-05-01), Ohkawa et al.
patent: 5352600 (1994-10-01), Gelfand et al.
patent: 5360523 (1994-11-01), Middendorf et al.
patent: 5365455 (1994-11-01), Tibbetts et al.
patent: 5418149 (1995-05-01), Gelfand et al.
patent: 5419825 (1995-05-01), Fujii
patent: 5427911 (1995-06-01), Ruano
patent: 5453355 (1995-09-01), Birkenmeyer et al.
patent: 5484701 (1996-01-01), Cocuzza et al.
patent: 5502773 (1996-03-01), Tibbetts et al.
patent: 5527898 (1996-06-01), Bauer et al.
patent: 5584983 (1996-12-01), Pruyn
patent: 5608063 (1997-03-01), Hobbs, Jr. et al.
patent: 5614386 (1997-03-01), Metzker et al.
patent: 5666435 (1997-09-01), Burgi et al.
patent: 5667971 (1997-09-01), Hochberg
patent: 5710628 (1998-01-01), Waterhouse et al.
patent: 5712476 (1998-01-01), Renfrew et al.
patent: 5733729 (1998-03-01), Lipshutz et al.
patent: 5751534 (1998-05-01), DeBalko
patent: 5776737 (1998-07-01), Dunn
patent: 5786142 (1998-07-01), Renfrew et al.
patent: 5789168 (1998-08-01), Leushner et al.
patent: 5821058 (1998-10-01), Smith et al.
patent: 5830657 (1998-11-01), Leushner et al.
patent: 5834189 (1998-11-01), Stevens et al.
patent: 5849542 (1998-12-01), Reeve et al.
patent: 5853979 (1998-12-01), Green et al.
patent: 5891632 (1999-04-01), Imai
patent: 5916747 (1999-06-01), Gilchrist et al.
patent: 5981186 (1999-11-01), Gabe et al.
patent: 6005663 (1999-12-01), Waterhouse et al.
patent: 6013444 (2000-01-01), Dau et al.
patent: 6027709 (2000-02-01), Little et al.
patent: 6068737 (2000-05-01), De Chamorro et al.
patent: 6083699 (2000-07-01), Leushner et al.
patent: 6195449 (2001-02-01), Bogden et al.
patent: 6208941 (2001-03-01), Marks
patent: 6303303 (2001-10-01), Green et al.
patent: 6397150 (2002-05-01), Izmailov
patent: 6404907 (2002-06-01), Gilchrist et al.
patent: 6413718 (2002-07-01), Leushner et al.
patent: 6428955 (2002-08-01), Koster et al.
patent: 6485625 (2002-11-01), Simpson et al.
patent: 6554987 (2003-04-01), Gilchrist et al.
patent: 6716394 (2004-04-01), Jensen et al.
patent: 2002/0147548 (2002-10-01), Walther et al.
patent: 2004/0072182 (2004-04-01), Lyamichev et al.
patent: 2004/0117130 (2004-06-01), Denisov et al.
patent: 2005/0042668 (2005-02-01), Perlin
patent: 4405251 (1994-08-01), None
patent: 0198403 (1986-10-01), None
patent: 0265293 (1988-04-01), None
patent: 0294524 (1988-12-01), None
patent: 0386859 (1990-09-01), None
patent: 0476712 (1992-03-01), None
patent: 0504943 (1992-09-01), None
patent: 0592060 (1994-04-01), None
patent: 0655506 (1995-05-01), None
patent: 2225139 (1990-05-01), None
patent: WO 8907149 (1989-08-01), None
patent: WO 9218650 (1992-10-01), None
patent: WO 9302212 (1993-02-01), None
patent: WO 9308305 (1993-04-01), None
patent: WO 9426894 (1994-11-01), None
patent: WO 9635810 (1994-11-01), None
patent: WO 9504140 (1995-02-01), None
patent: WO 9506756 (1995-03-01), None
patent: WO 9511961 (1995-05-01), None
patent: WO 9601008 (1996-01-01), None
patent: WO 9601909 (1996-01-01), None
patent: WO 9702488 (1997-01-01), None
patent: WO 9740184 (1997-10-01), None
patent: WO 9741259 (1997-11-01), None
patent: WO 9800708 (1998-01-01), None
patent: WO 9811258 (1998-03-01), None
patent: WO 9824930 (1998-06-01), None
patent: WO 9841650 (1998-09-01), None
patent: WO 0000637 (2000-01-01), None
patent: WO 0068410 (2000-11-01), None
Andersson, et al., “Adaptor-Based Uracil DNA Glycosylase Cloning Simplifies Shotgun Library Construction for Large-Scale Sequencing”,Analytical Biochemistry218: 300-308 (1994).
Arnot, et al., “Digital codes from hypervariable tandemly repeated DNA sequences in thePlasmodium falciparumcircumsporozoite gene can genetically barcode isolates”,Molecular and Biochemical Parasitology61: 15-24 (1993).
Beebe, et al., “Incidence ofNeisseria gonorrhoeaeIsolates Negative by Syva Direct Fluorescent-Antibody Test but Positive by Gen-Probe Accuprobe Test in a Sexually Transmitted Disease Clinic Population”,Journal of Clinical Microbiology31(9):2535-2537 (Sep. 1993).
Bej, et al., “Detection of Coliform Bacteria andEscherichia coliby Multiplex Polymerase Chain Reaction: Comparison with Defined Substrate and Plating Methods for Water Quality Monitoring”,Applied and Environmental Microbiology57(8): 2429-2432 (Aug. 1991).
Bej et al., “Multiplex PCR amplification and immobilized capture probes for detection of bacterial pathogens and indicators in water”,Molecular Cellular Probes4: 353-365 (1990).
Bowling, et al., “Neighboring Nucleotide Interactions During DNA Sequencing Electrophoresis”,Nucleic Acids Research19: 3089-3097 (1991). (Abstract only.).
Carothers, et al., “Point Mutation Analysis in a Mammalian Gene: Rapid Preparation of Total RNA, PCR Amplification of cDNA, andTaqSequencing by a Novel Method”,BioTechniques7(5):494-498 (May 1989).
Church, et al., “Genomic Sequencing”,Proc. Natl. Acad. Sci. USA81: 1991-1995 (1984).
Church, et al., “The Genomic Sequencing Technique”,Medical Genetics: Past, Present, Future, pp. 17-21 (1985).
De Schryver, et al., “Epidemiology of sexually transmitted diseases: the global picture”,Bulletin of the World Health Organization68:639-654 (1990).
Dear, et al., “A sequence assembly and editing program for efficient management of large projects”,Nucleic Acids Research19(14): 3907-3911 (1991).
Deng, et al., “Simultaneous amplification and sequencing of genomic DNA (SAS): sequencing of 16S rRNA genes using total genomic DNA FromButyrivibrio fibrisolvens, and detection and genotyping of nonculturable mycoplasma-l

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