Method and apparatus for analysis of chromatographic migration patterns
AssigneeUniversity of Utah Research Foundation
InventorAndrew F. Marks
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Abstract
The present invention includes a method and apparatus for the detection and analysis of information-containing signals in chromatographic data using iterative blind deconvolution and fuzzy logic algorithms. The invented method analyzes chromatographic data from a wide variety of sources of DNA sequencing information, including gel and capillary electrophoresis. Autoradiograms, single-fluor, four-lane and four fluor, single lane fluorescent chromatographic data are suitable sources of unprocessed input data. The output from the invented base calling method includes called (identified) sequence data and quality values for the called bases.
Claims19
A computer-implemented method for determining base identity in unprocessed nucleic acid sequencing data, comprising the steps of:
- receiving unprocessed input data comprising unprocessed nucleic acid sequencing data;
- preprocessing said input data to generate preprocessed data;
- blind deconvolving said preprocessed data to generate blind deconvolved data;
- extranormalizing said blind deconvolved data to generate extranormalized data;
- detecting peaks in said extranormalized data using peak detection means to generate processed data;
- editing the quality of said processed data using fuzzy logic editing means to generate called nucleotide sequence and at least one quality value for said called sequence.
A computer-implemented method for identifying DNA sequence in unprocessed nucleic acid sequencing data, comprising the steps of:
- receiving unprocessed input data comprising unprocessed nucleic acid sequencing data;
- preprocessing said input data to generate preprocessed data;
- blind deconvolving said preprocessed data to generate blind deconvolved data;
- extranorrnalizing said blind deconvolved data to generate extranormalized data;
- detecting peaks in said extranormalized data to generate peak detected-data;
- identifying and removing insertions in said peak detected-data using a fuzzy logic insertion detection algorithm;
- identifying and filling gaps in said peak detected-data using a fuzzy logic gap checking algorithm;
- and
- producing processed sequence data.
A computer-implemented method of determining a nucleotide sequence of a DNA molecule comprising:
- providing a set of lane signals encoding the migration pattern of a DNA molecule subjected to DNA sequence analysis to generate an input data;
- preprocessing said input data to generate preprocessed data, said preprocessing comprising at least one of the following steps:
- identifying Begin and End points,
- subtracting baseline noise,
- spectrally separating said input data using a separation matrix to correct for spectral cross-talk, and
- leakage separating said input data using a separation matrix to correct for lane leakage;
- blind deconvolving said preprocessed data to generate blind deconvolved data, said blind deconvolving deblurring signals in said preprocessed data and normalizing signal amplitudes, said blind deconvolving using an iterative filter band width algorithm;
- extranormalizing said blind deconvolved data to generate extranormalized data, said extranormalizing including at least one of the following steps:
- correcting relative signal mobility differences using a Monte Carlo alignment, and
- attenuating signals accentuated by blind deconvolution;
- detecting peaks in said extranormalized data to generate peak detected-data;
- identifying and removing insertions in said peak-detected data using a fuzzy logic insertion detection algorithm;
- identifying and filling gaps in said peak-detected data using a fuzzy logic gap checking algorithm;
- and
- producing processed sequence data.
Dependencies are inferred from the claim text.