DNA sequencing

DNA sequencesequencesequencingsequencedsequencesnext generation sequencinggene sequencingnext-generation sequencingDNA samplinggenetic sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA.wikipedia
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Protein

proteinsproteinaceousstructural proteins
DNA sequencing is also the most efficient way to indirectly sequence RNA or proteins (via their open reading frames).
The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code.

Gene

genesnumber of genesgene sequence
DNA sequencing may be used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes, or entire genomes of any organism.
The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool.

DNA

deoxyribonucleic aciddouble-stranded DNAdsDNA
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA.
A DNA sequence is called a "sense" sequence if it is the same as that of a messenger RNA copy that is translated into protein.

Frederick Sanger

Fred SangerSangerFrederic Sanger
The foundation for sequencing proteins was first laid by the work of Frederick Sanger who by 1955 had completed the sequence of all the amino acids in insulin, a small protein secreted by the pancreas. The chain-termination method developed by Frederick Sanger and coworkers in 1977 soon became the method of choice, owing to its relative ease and reliability.
In 1980, Walter Gilbert and Sanger shared half of the chemistry prize "for their contributions concerning the determination of base sequences in nucleic acids".

Metagenomics

metagenomicmetagenomemetagenomes
The field of metagenomics involves identification of organisms present in a body of water, sewage, dirt, debris filtered from the air, or swab samples from organisms.
In 2005 Stephan C. Schuster at Penn State University and colleagues published the first sequences of an environmental sample generated with high-throughput sequencing, in this case massively parallel pyrosequencing developed by 454 Life Sciences.

Recombinant DNA

recombinantrecombinant proteingene splicing
Advancements in sequencing were aided by the concurrent development of recombinant DNA technology, allowing DNA samples to be isolated from sources other than viruses.
Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome.

Human genome

genomehuman DNAhuman geneticist
The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of complete DNA sequences, or genomes, of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, plant, and microbial species.
However, there are still numerous gaps in the heterochromatic parts of the genome which is much harder to sequence due to numerous repeats and other intractable sequence features.

Applied Biosystems

ABIApplied Biosystems, Inc.PE Biosystems
This was followed by Applied Biosystems' marketing of the first fully automated sequencing machine, the ABI 370, in 1987 and by Dupont's Genesis 2000 which used a novel fluorescent labeling technique enabling all four dideoxynucleotides to be identified in a single lane. Emulsion PCR is used in the methods developed by Marguilis et al. (commercialized by 454 Life Sciences), Shendure and Porreca et al. (also known as "polony sequencing") and SOLiD sequencing, (developed by Agencourt, later Applied Biosystems, now Life Technologies).
Through the 1980s and early 1990s, Applied Biosystems, Inc. operated independently and manufactured biochemicals and automated genetic engineering and diagnostic research instruments, including the principal brand of DNA sequencing machine used by the Human Genome Project consortium centers.

DNA sequencer

DNA sequencersautomated DNA sequencerDNA sequencing instruments
Following the development of fluorescence-based sequencing methods with a DNA sequencer, DNA sequencing has become easier and orders of magnitude faster.
A DNA sequencer is a scientific instrument used to automate the DNA sequencing process.

Pyrosequencing

Biotage454 pyrosequencingBiotage Pyrosequencer
In 1996, Pål Nyrén and his student Mostafa Ronaghi at the Royal Institute of Technology in Stockholm published their method of pyrosequencing.
Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle, in which the sequencing is performed by detecting the nucleotide incorporated by a DNA polymerase.

Sewage

raw sewagedomestic sewagedrainage system
The field of metagenomics involves identification of organisms present in a body of water, sewage, dirt, debris filtered from the air, or swab samples from organisms.

Allan Maxam

Walter Gilbert and Allan Maxam at Harvard also developed sequencing methods, including one for "DNA sequencing by chemical degradation".
He was one of the contributors to develop a DNA sequencing method at Harvard University, while working as a student in the laboratory of Walter Gilbert.

Molecular biology

molecular biologistmolecularmolecular microbiology
Sequencing is used in molecular biology to study genomes and the proteins they encode.
In brief, PCR allows a specific DNA sequence to be copied or modified in predetermined ways.

Sanger sequencing

chain termination methodSanger methodSanger
The chain-termination method developed by Frederick Sanger and coworkers in 1977 soon became the method of choice, owing to its relative ease and reliability.
Sanger sequencing is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication.

Genomics

genomicgenome biologygenomic analysis
The Sanger method, in mass production form, is the technology which produced the first human genome in 2001, ushering in the age of genomics.
Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.

Genetic testing

DNA testingDNA analysisDNA test
This is a form of genetic testing, though some genetic tests may not involve DNA sequencing.
The sample is sent to a laboratory where technicians look for specific changes in chromosomes, DNA, or proteins, depending on the suspected disorders, often using DNA sequencing.

Polymerase chain reaction

PCRPCR amplificationpolymerase chain reaction (PCR)
The DNA sample preparation and random surface-polymerase chain reaction (PCR) arraying methods described in this patent, coupled to Roger Tsien et al.'s "base-by-base" sequencing method, is now implemented in Illumina's Hi-Seq genome sequencers.
Applications of the technique include DNA cloning for sequencing, gene cloning and manipulation, gene mutagenesis; construction of DNA-based phylogenies, or functional analysis of genes; diagnosis and monitoring of hereditary diseases; amplification of ancient DNA; analysis of genetic fingerprints for DNA profiling (for example, in forensic science and parentage testing); and detection of pathogens in nucleic acid tests for the diagnosis of infectious diseases.

Phred quality score

PhredPhred scorephred-scaled base
In 1998, Phil Green and Brent Ewing of the University of Washington described their phred quality score for sequencer data analysis, a landmark analysis technique that gained widespread adoption, and which is still the most common metric for assessing the accuracy of a sequencing platform.
A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing.

Sequence assembly

genome assemblyassembledassembly
Short DNA fragments purified from individual bacterial colonies are individually sequenced and assembled electronically into one long, contiguous sequence.
This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used.

454 Life Sciences

454454 sequencing454 technology
Emulsion PCR is used in the methods developed by Marguilis et al. (commercialized by 454 Life Sciences), Shendure and Porreca et al. (also known as "polony sequencing") and SOLiD sequencing, (developed by Agencourt, later Applied Biosystems, now Life Technologies).
454 Life Sciences was a biotechnology company based in Branford, Connecticut that specialized in high-throughput DNA sequencing.

Mostafa Ronaghi

In 1996, Pål Nyrén and his student Mostafa Ronaghi at the Royal Institute of Technology in Stockholm published their method of pyrosequencing.
Mostafa Ronaghi (born 1968) is an Iranian molecular biologist, specializing in DNA sequencing methodology.

ABI Solid Sequencing

SOLiDABI SOLiDABI/SOLiD sequencing
Emulsion PCR is used in the methods developed by Marguilis et al. (commercialized by 454 Life Sciences), Shendure and Porreca et al. (also known as "polony sequencing") and SOLiD sequencing, (developed by Agencourt, later Applied Biosystems, now Life Technologies).
SOLiD (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation DNA sequencing technology developed by Life Technologies and has been commercially available since 2006.

Massively parallel signature sequencing

Lynx Therapeutics' Massively Parallel Signature Sequencing (MPSS)
Lynx Therapeutics published and marketed massively parallel signature sequencing (MPSS), in 2000.
Massive parallel signature sequencing (MPSS) is a procedure that is used to identify and quantify mRNA transcripts, resulting in data similar to serial analysis of gene expression (SAGE), although it employs a series of biochemical and sequencing steps that are substantially different.

Shotgun sequencing

shotgunwhole genome shotgun sequencingpaired end sequencing
The different strategies have different tradeoffs in speed and accuracy; shotgun methods are often used for sequencing large genomes, but its assembly is complex and difficult, particularly with sequence repeats often causing gaps in genome assembly.
The chain termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs.

ChIP-sequencing

ChIP-seq(ChIP-Seq)
High-throughput, or next-generation, sequencing applies to genome sequencing, genome resequencing, transcriptome profiling (RNA-Seq), DNA-protein interactions (ChIP-sequencing), and epigenome characterization.
ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.