System and method for consensus-calling with per-base...

Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical

Reexamination Certificate

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C435S006120

Reexamination Certificate

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07406385

ABSTRACT:
The present teachings disclose a method for evaluation of a polynucleotide sequence using a consensus-based analysis approach. The sequence analysis method utilizes quality values for a plurality of aligned sequence fragments to identify consensus basecalls and calculate associated consensus quality values. The disclosed method is applicable to resolution of single nucleotide polymorphisms, mixed-based sequences, heterozygous allelic variants, and heterogeneous polynucleotide samples.

REFERENCES:
patent: 6681186 (2004-01-01), Denisov et al.
Huang, X. and Mada A. “CAP3: A DNA Sequence Assembly Program,”Genome Research, vol. 9, 1999, pp. 868-877.
Nickerson, Deborah A. et al. “PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing,”Nucleic Acids Research, Oxford University Press, Surrey, GB, vol. 25, No. 14, 1997, pp. 2745-2751.
Staden, R. “Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing”,Nucleic Acids Research, Oxford University Press, Surrey, GB, vol. 10, No. 15; Aug. 11, 1982, pp. 4731-4751.
Bonfield, J.K. et al. “The application of numerical estimates of base calling accuracy to DNA sequencing projects”,Nucleic Acids Research, Oxford University Press, Surrey, GB, vol. 23, No. 8, 1995, pp. 1406-1410.
Ewing, B. et al. “Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment,”Genome Research, Cold Spring Harbor Laboratory Press, US, vol. 8, 1998, pp. 175-185.
Ewing, B. et al. “Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities,”Genome Research, Cold Spring Harbor Laboratory Press, U.S., vol. 8, 1998, pp. 186-194.
Allex, C.F. et al. “Neural network input representations that produce accurate consensus sequences from DNA fragment assemblies,”Bioinformatics, Oxford, vol. 15, No. 9, Sep. 1999, pp. 723-728.
Gordon, David et al. “Consed: A Graphical Tool for Sequence Finishing,”Genome Research, vol. 8, No. 3, Mar. 1998, pp. 195-202.

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