A method to determine the filter matrix in four‐dye fluorescence‐based DNA sequencing

Huang, Weian; Yin, Zhongbin; States, David J.; Thomas, Lewis J.; Fuhrmann, D.R.

doi:10.1002/elps.1150180106

Cited by 10 publications

(9 citation statements)

References 5 publications

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“…The difference between matrices (6) and (7) is larger than that between matrices (4) and (5), especially in the fourth column. 1 333 ±12 14 203 ±1 3 70 0 10 115 ±3 11 2 330 0 7 412 1 4 209 5 12 139 4 26 3 241 9 10 296 0 4 544 ±3 16 183 ±4 17 4 96 2 6 88 0 4 176 ±2 6 562 3 50 Figure 4.…”

Section: Other Estimatesmentioning

confidence: 88%

“…The middle plot shows the color-corrected data using the matrix in (4). The bottom plot shows the color-corrected data using the matrix in (6). The representation for the color-correction data is the following: green, C; black, G; red, A; blue, T.…”

Section: Other Estimatesmentioning

confidence: 99%

“…The quality of the estimated matrix is evaluated by examining the 3-D scatter plot of the transformed peak points in the training data set. Huang et al [6] use a variant of a standard iterative clustering technique for feature selection in pattern recognition to determine the crosstalk matrix. This method requires less preprocessing of the data than the method in Yin et al [3], but it requires the baseline be subtracted and an initial value for the iterative algorithm.…”

Section: Introductionmentioning

confidence: 99%

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An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing

Speed

1999

Electrophoresis

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Section: Other Estimatesmentioning

confidence: 88%

Section: Other Estimatesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing

Speed

1999

Electrophoresis

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“…Of these, determination of the cross-talk matrix, which allows for the conversion of mixed-fluorescent signals into concentration estimates for the dye-labeled DNA fragments at a given time point during a sequencing experiment, is likely the most relevant operation (21). Numerous research groups have described methods to determine a representative cross-talk matrix for DNA sequencing data, albeit with limited success (22)(23)(24)(25)(26)(27)(28). For comparison, we present an Applied Biosystems cross-talk matrix for the BigDye v3.1 terminator chemistry derived from a model 377 DNA sequencer ( Table 2) that shows significantly higher off-diagonal values.…”

Section: Pme Technologymentioning

confidence: 99%

Color-blind fluorescence detection for four-color DNA sequencing

Lewis

Haaland

Nguyen

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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We present an approach called pulsed multiline excitation (PME) for measurements of multicomponent, fluorescence species and demonstrate its application in capillary electrophoresis for DNA sequencing. To fully demonstrate the advantages of PME, a fluorescent dye set has been developed whose absorption maxima span virtually the entire visible spectrum. Unlike emission wavelength-dependent approaches for identifying fluorescent species, the removal of the spectral component in PME confers a number of advantages including higher and normalized signals from all dyes present in the assay, the elimination of spectral cross-talk between dyes, and higher signal collection efficiency. Base-calling is unambiguously determined once dye mobility corrections are made. These advantages translate into significantly enhanced signal quality as illustrated in the primary DNA sequencing data and provide a means for achieving accurate base-calling at lower reagent concentrations.

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“…Since publication, the only changes to the program have been a port to OpenStep to increase portability (described below) and some user interface additions. Since the time of that work further refinement of the multicomponent algorithm has been performed in another laboratory (Huang et al 1997). The program will be described briefly below in conjunction with the related multicomponent transform step that is part of BaseFinder.…”

mentioning

confidence: 99%

A Software System for Data Analysis in Automated DNA Sequencing

Giddings¹,

Severin²,

Westphall³

et al. 1998

Genome Res.

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Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and GelImager, is described. BaseFinder is a framework for trace processing, analysis, and base-calling. BaseFinder is highly extensible, allowing the addition of trace analysis and processing modules without recompilation. Powerful scripting capabilities combined with modularity and multilane handling allow the user to customize BaseFinder to virtually any type of trace processing. We have developed an extensive set of data processing and analysis modules for use with the program in fluorescence-based sequencing. GelImager is a framework for gel image manipulation. It can be used for gel visualization, lane retracking, and as a front end to the Washington University Getlanes program. The programs were designed using a cross-platform development environment, currently allowing them to run in Windows NT, Windows 95, Openstep/Mach, and Rhapsody. Work is ongoing to deploy the software on additional platforms, including Solaris, Linux, and MacOS. This software has been thoroughly tested and debugged in the analysis of >2 million bp of raw sequence data from human chromosome 19 region q13. Overall sequencing accuracy was measured using a significant subset of these data, consisting of ∼600 sequences, by comparing the individual shotgun sequences against the final assembled contigs. Also, results are reported from experiments that analyzed the accuracy of the software and two other well-known base-calling programs for sequencing the M13mp18 vector sequence.[The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF025422]

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A method to determine the filter matrix in four‐dye fluorescence‐based DNA sequencing

Cited by 10 publications

References 5 publications

An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing

An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing

Color-blind fluorescence detection for four-color DNA sequencing

A Software System for Data Analysis in Automated DNA Sequencing

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