Nucleotide sequence of bacteriophage λ DNA

Sanger, F.; Coulson, Alan; Hong, Guofan; Hill, Daniel H.; Petersen, George B.

doi:10.1016/0022-2836(82)90546-0

Cited by 1,126 publications

(302 citation statements)

References 48 publications

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“…It is hoped that the platypus genome, which is very recently decoded in 2008, would provide a valuable resource for in-depth comparative analysis of mammals [9]. [10] method is well known and most commonly used for reading genome sequences. It uses Gel electrophoresis that facilitates reading the bases due to reaction of the fluorescent dye staining different bases differently.…”

Section: Why Is It Important Tomentioning

confidence: 99%

An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function

Kikuchi

Chakraborty

2012

Applied Computational Intelligence and Soft Computing

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To decode a long genome sequence, shotgun sequencing is the state-of-the-art technique. It needs to properly sequence a very large number, sometimes as large as millions, of short partially readable strings (fragments). Arranging those fragments in correct sequence is known as fragment assembling, which is an NP-problem. Presently used methods require enormous computational cost. In this work, we have shown how our modified genetic algorithm (GA) could solve this problem efficiently. In the proposed GA, the length of the chromosome, which represents the volume of the search space, is reduced with advancing generations, and thereby improves search efficiency. We also introduced a greedy mutation, by swapping nearby fragments using some heuristics, to improve the fitness of chromosomes. We compared results with Parsons' algorithm which is based on GA too. We used fragments with partial reads on both sides, mimicking fragments in real genome assembling process. In Parsons' work base-pair array of the whole fragment is known. Even then, we could obtain much better results, and we succeeded in restructuring contigs covering 100% of the genome sequences.

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Section: Why Is It Important Tomentioning

confidence: 99%

An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function

Kikuchi

Chakraborty

2012

Applied Computational Intelligence and Soft Computing

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“…Genomic DNA fragments identified by plaque hybridization or PCR amplification were recloned into either pUC19 or pBluescript II SK(-). DNA sequences were determined for both strands by the method of Sanger et al (1982) with a BcaBEST dideoxy sequencing kit (Takara, Kyoto, Japan).…”

Section: Isolation and Characterization Of Genomic Clonesmentioning

confidence: 99%

Extreme heterogeneous composition of the Paramecium caudatum macronuclear genomic DNA between hemoglobin and nucleosome assembly protein-1 genes

et al. 2010

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The intergenic region between the hemoglobin (hb) and nucleosome assembly protein-1 (nap-1) genes in the Paramecium caudatum macronuclear genome was previously found to be heterogeneously composed. Cloning of this intergenic region from the macronuclear genomic DNA identified four unique DNA fragments of different sizes. Sequencing of the cloned fragments revealed extreme heterogeneity and characteristics of both internal eliminated sequence (IES) and imprecise internal deletion sequences (IIDSs) in the intergenic region. Missing sequences were an AT-rich and direct repeats existed in their boundaries. Southern blotting of the total genomic DNA and polymerase chain reaction (PCR) of the total genomic DNAs indicated that there exist a dozen DNA fragments of different sizes in this intergenic region. It is likely that the heterogeneity found in the P. caudatum macronuclear genome results from the variable removal of an intergenic region.

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“…Table 1 outlines these and other model organism projects discussed in this review, and the strategies they employ. These include 'shotgun' sequencing (used by Fred Sanger to sequence the 48.5 kb bacteriophage genome in 1982 [5]) using a range of sources of DNA and multiplex walking using genomic DNA [6,7]. The E. coli pilot project worked from a physical map of overlapping lambda clones [8].…”

Section: Historical Perspectivesmentioning

confidence: 99%

Yeasties and beasties: 7 years of genome sequencing

Thomas

1996

FEBS Letters

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Xbstract The Saccharomyces cerevisiae genome sequencing project was the first of many projects aimed at sequencing the entire genomes of model organisms. Since its initiation in 1989, there have been numerous debates about the validity of genome ~equencing, especially with reference to the model organisms. .',;even years on, I hope to satisfy some of the critics by demonstrating that, as a consequence of the mass of data now becoming available from such projects, and the beginning of the major collaborative effort to sequence the human genome, we are now entering an exciting and dynamic time for those involved not only in genome sequencing, but also in all areas of the biological ,ciences.

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Nucleotide sequence of bacteriophage λ DNA

Cited by 1,126 publications

References 48 publications

An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function

An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function

Extreme heterogeneous composition of the Paramecium caudatum macronuclear genomic DNA between hemoglobin and nucleosome assembly protein-1 genes

Yeasties and beasties: 7 years of genome sequencing

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