A review of DNA sequencing techniques

França, Lilian T. C.; Carrilho, Emanuel; Kist, Tarso B. Ledur

doi:10.1017/s0033583502003797

Cited by 197 publications

(122 citation statements)

References 162 publications

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“…At present, the Pyrosequencing technology is limited to reads of up to 100 nucleotides [4]; however, efforts are under way to increase the read length. In contrast, the Sanger dideoxy sequencing method has average read lengths of 400-600 bases [12], and there are reports of Sanger sequencing reads of over 1000 bases [2].…”

Section: Discussionmentioning

confidence: 99%

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Large‐scale Pyrosequencing of synthetic DNA: A comparison with results from Sanger dideoxy sequencing

et al. 2006

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Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequencing against the current gold standard, Sanger dideoxy sequencing. Starting with yeast genomic DNA, parallel PCR amplification methods were used to prepared 4747 short barcode-containing constructs from 6000 Saccharomyces cerevisiae gene-deletion strains. Pyrosequencing was optimized for average read lengths of 25-30 bases, which included in each case a 20-mer barcode sequence. Results were compared with sequence data obtained by the standard Sanger dideoxy chain termination method. In most cases, sequences obtained by Pyrosequencing and Sanger dideoxy sequencing were of comparable accuracy, and the overall rate of failure was similar. The DNA in the barcodes is derived from synthetic oligonucleotide sequences that were inserted into yeast-deletion-strain genomic DNA by homologous recombination and represents the most significant amount of DNA from a synthetic source that has been sequenced to date. Although more automation and quality control measures are needed, Pyrosequencing was shown to be a fast and convenient method for determining short stretches of DNA sequence.

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Section: Discussionmentioning

confidence: 99%

“…DNA sequencing is used in such diverse areas as molecular biology, genetics, biotechnology, pharmacology, forensics, archeology, and anthropology. Given the new discoveries it continues to generate, DNA sequencing will continue to revolutionize the conceptual foundations of many sciences [2].…”

Section: Introductionmentioning

confidence: 99%

Large‐scale Pyrosequencing of synthetic DNA: A comparison with results from Sanger dideoxy sequencing

et al. 2006

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“…It's helpful for human recognition, which is used in genetic testing and fingerprint, is unique for every person. There are several techniques for DNA sequence like MaxamGilbert sequencing in (1977) by Allan Maxamand Walter Gilbert and Sanger Sequencing, the popular technique for DNA sequence, by Fredrick Sangerat (1977) (França et al, 2002). These techniques depend on a number of bases.…”

Section: Introductionmentioning

confidence: 99%

Swarm Optimization Techniques for Segmenting Gel Electrophoresis Images

Ibrahim¹,

Makhlouf²,

El-Tawel³

et al. 2016

American Journal of Bioinformatics

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Gel Electrophoresis (GE) are discussed as the main tool to dissociate DNA sequences. It helps in analyzing the genome such that each image resulting from it consists of lanes that include several bands. Image segmentation plays the foremost role in image processing. It helps in producing accurate results in medical diagnosis. Image segmentation works by dividing an image into regions that cover the full image. Image segmentation methods can be implemented, but still have certain defects that cannot produce accurate results. On the other hand, Swarm Optimization methods produce results with high efficiency in image segmentation. In this study, swarm optimization techniques for image segmentation are proposed. The proposed technique depends on applying different segmentation methods as Fuzzy C-Means (FCM) and Particle Swarm Optimization (PSO) is an extensively used in computer science considered a simple and easy algorithm to implement. It also depends on swarm intelligence. PSO useful in image segmentation because the result is more exact and efficient. Furthermore, Darwinian PSO (DPSO) and Fractional Order Darwinian PSO (FODPSO) produced precise results. The efficiency of the proposed approach is compared with other by computing image quality measurement parameters like Peak Signal to Noise Ratio (PSNR), Mean Square Error (MSE) and others. The proposed technique, especially FODPSO produces more accurate results to segment GE image.

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“…It is expected that discovery and massive screening of DNA polymorphisms will become essential for taylor-made drugs as well as disease gene association studies. Among the various experimental techniques for detection of DNA variations, DNA sequencing is the most universal approach [1]. Although sequencing has been the "golden standard" for a number of years, a variety of alternative approaches for detection and screening has emerged, overcoming the high cost and occasional lack of sensitivity.…”

Section: Introductionmentioning

confidence: 99%

Cycling gradient capillary electrophoresis: A low‐cost tool for high‐throughput analysis of genetic variations

et al. 2003

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In the present work, we introduce a new type of DNA variation detection. This method represents a transfer of melting gel technique onto multicapillary electrophoresis DNA sequencing instrument with further improvements to achieve maximum sample throughput while maintaining a high performance. The main improvement comes from application of cycling (revolving) temporal temperature gradient in place of a single-sweep gradient, commonly used in similar gel-based techniques. This improvement enables utilization of multiple-injection technique, in which multiple samples are injected into the same capillary (or sets of capillaries) separated by predefined time intervals of partial electrophoresis. The periodic oscillation of the temperature results in identical separation conditions of all samples injected in such series. Using this novel approach, we demonstrate a dramatic increase in separation throughput by turning a standard commercial 96-capillary array instrument into a semicontinuous flow mutation detection system capable to screen over 15 000 samples in 24 h of operation on a single 96-capillary commercial instrument. This represents a 10-fold increase in sample throughput over the current comparable technology.

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A review of DNA sequencing techniques

Cited by 197 publications

References 162 publications

Large‐scale Pyrosequencing of synthetic DNA: A comparison with results from Sanger dideoxy sequencing

Large‐scale Pyrosequencing of synthetic DNA: A comparison with results from Sanger dideoxy sequencing

Swarm Optimization Techniques for Segmenting Gel Electrophoresis Images

Cycling gradient capillary electrophoresis: A low‐cost tool for high‐throughput analysis of genetic variations

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