WO2003029487A3 - Dna sequencer - Google Patents

Dna sequencer Download PDF

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Publication number
WO2003029487A3
WO2003029487A3 PCT/GB2002/004398 GB0204398W WO03029487A3 WO 2003029487 A3 WO2003029487 A3 WO 2003029487A3 GB 0204398 W GB0204398 W GB 0204398W WO 03029487 A3 WO03029487 A3 WO 03029487A3
Authority
WO
WIPO (PCT)
Prior art keywords
model
traces
program
dataset
penalty function
Prior art date
Application number
PCT/GB2002/004398
Other languages
French (fr)
Other versions
WO2003029487A2 (en
Inventor
Aled Wynne Jones
Peter John Kelly
Daniel Reginald Ewart Timson
Mike Raymond Reynolds
Nicholas Vasilopoulos
Original Assignee
Scient Generics Ltd
Aled Wynne Jones
Peter John Kelly
Daniel Reginald Ewart Timson
Mike Raymond Reynolds
Nicholas Vasilopoulos
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from GB0123875A external-priority patent/GB0123875D0/en
Application filed by Scient Generics Ltd, Aled Wynne Jones, Peter John Kelly, Daniel Reginald Ewart Timson, Mike Raymond Reynolds, Nicholas Vasilopoulos filed Critical Scient Generics Ltd
Priority to AU2002329425A priority Critical patent/AU2002329425A1/en
Publication of WO2003029487A2 publication Critical patent/WO2003029487A2/en
Publication of WO2003029487A3 publication Critical patent/WO2003029487A3/en

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

A carrier carries a computer program for base calling DNA bases from a dataset corresponding to observed traces obtained from electrophoresis. The program generates a database in the computer memory corresponding to a model of a DNA sequence and refines the model of the DNA sequence by the following operations: (a) making a change to the base sequence of the model; (b) predicting the form of the traces from the modified model; (c) comparing the predicted traces with the observed traces in dataset to generate a penalty function; (d) determining whether or not to accept the modified model based on the value of the penalty function; and (e) repeating operations (a) to (d) until termination criteria have been achieved. The program has the advantage that it is less empirical and dependent on experimental setup than existing programs such as Phred.
PCT/GB2002/004398 2001-10-04 2002-09-30 Dna sequencer WO2003029487A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002329425A AU2002329425A1 (en) 2001-10-04 2002-09-30 Dna sequencer

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
GB0123875.7 2001-10-04
GB0123875A GB0123875D0 (en) 2001-10-04 2001-10-04 Noise reduction
GB0216746A GB0216746D0 (en) 2001-10-04 2002-07-18 DNA sequencer
GB0216746.8 2002-07-18

Publications (2)

Publication Number Publication Date
WO2003029487A2 WO2003029487A2 (en) 2003-04-10
WO2003029487A3 true WO2003029487A3 (en) 2004-05-27

Family

ID=26246613

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2002/004398 WO2003029487A2 (en) 2001-10-04 2002-09-30 Dna sequencer

Country Status (2)

Country Link
AU (1) AU2002329425A1 (en)
WO (1) WO2003029487A2 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7647188B2 (en) * 2004-09-15 2010-01-12 F. Hoffmann-La Roche Ag Systems and methods for processing nucleic acid chromatograms
CN111462818B (en) * 2019-01-22 2023-04-21 武汉华大医学检验所有限公司 Sequencing yield prediction method, and method and device for establishing sequencing yield prediction model

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998011258A1 (en) * 1996-09-16 1998-03-19 University Of Utah Research Foundation Method and apparatus for analysis of chromatographic migration patterns
US5916747A (en) * 1995-06-30 1999-06-29 Visible Genetics Inc. Method and apparatus for alignment of signals for use in DNA based-calling
US6218121B1 (en) * 1995-05-09 2001-04-17 Curagen Corporation Apparatus and method for the generation, separation, detection, and recognition of biopolymer fragments
US6236944B1 (en) * 1998-04-16 2001-05-22 Northeastern University Expert system for analysis of DNA sequencing electropherograms

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6218121B1 (en) * 1995-05-09 2001-04-17 Curagen Corporation Apparatus and method for the generation, separation, detection, and recognition of biopolymer fragments
US5916747A (en) * 1995-06-30 1999-06-29 Visible Genetics Inc. Method and apparatus for alignment of signals for use in DNA based-calling
WO1998011258A1 (en) * 1996-09-16 1998-03-19 University Of Utah Research Foundation Method and apparatus for analysis of chromatographic migration patterns
US6236944B1 (en) * 1998-04-16 2001-05-22 Northeastern University Expert system for analysis of DNA sequencing electropherograms

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
EWING B ET AL: "BASE-CALLING OF AUTOMATED SEQUENCER TRACES USING PHRED. I. ACCURACYASSESSMENT", GENOME RESEARCH, COLD SPRING HARBOR LABORATORY PRESS, US, vol. 8, 1998, pages 175 - 185, XP000915054, ISSN: 1088-9051 *

Also Published As

Publication number Publication date
AU2002329425A1 (en) 2003-04-14
WO2003029487A2 (en) 2003-04-10

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