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Read (biology)
In DNA sequencing, a read is an inferred sequence of base pairs (or base pair probabilities) corresponding to all or part of a single DNA fragment. A typical sequencing experiment involves DNA fragmentation, fragmentation of the genome into millions of molecules, which are size-selected and ligation (molecular biology), ligated to adapter (genetics), adapters. The set of fragments is referred to as a sequencing library, which is sequenced to produce a set of reads. Read length Sequencing technologies vary in the length of reads produced. Reads of length 20-40 base pairs (bp) are referred to as ultra-short. Typical sequencers produce read lengths in the range of 100-500 bp. However, Pacific Biosciences platforms produce read lengths of approximately 1500 bp. Read length is a factor which can affect the results of biological studies. For example, longer read lengths improve the resolution of ''de novo'' genome assembly and detection of structural variants. It is estimated that read ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, thymine, cytosine, and guanine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, Genographic Project, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged. The rapid advancements in DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base Pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The Complementarity (molecular biology), complementary nature of this based-paired structure provides a Redundancy (information theory), redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Fragmentation
DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously. Spontaneous or accidental DNA fragmentation is fragmentation that gradually accumulates in a cell. It can be measured by e.g. the comet assay or by the TUNEL assay. Its main units of measurement is the DNA Fragmentation Index (DFI). A DFI of 20% or more significantly reduces the success rates after ICSI. DNA fragmentation was first documented by Williamson in 1970 when he observed discrete oligomeric fragments occurring during cell death in primary neonatal liver cultures. He described the cytoplasmic DNA isolated from mouse liver cells after culture as characterized by DNA fragments with a molecular weight consisting of multiples of 135 kDa. This finding was consistent with the hypothesis that these DNA fragments were a specific degradation product of nuclear DNA. Intentional DNA fragmentation is often neces ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligation (molecular Biology)
Ligation is the joining of two nucleotides, or two nucleic acid fragments, into a single polymeric chain through the action of an enzyme known as a ligase. The reaction involves the formation of a phosphodiester bond between the 3'-hydroxyl terminus of one nucleotide and the 5'-phosphoryl terminus of another nucleotide, which results in the two nucleotides being linked consecutively on a single strand. Ligation works in fundamentally the same way for both DNA and RNA. A cofactor is generally involved in the reaction, usually Adenosine triphosphate, ATP or Nicotinamide riboside, NAD+. Eukaryotic ligases belong to the ATP type, while the NAD+ type are found in bacteria (e.g. Escherichia coli, ''E. coli''). Ligation occurs naturally as part of numerous cellular processes, including DNA replication, transcription, splicing, and recombination, and is also an essential laboratory procedure in molecular cloning, whereby DNA fragments are joined to create recombinant DNA molecules (such a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Adapter (genetics)
An adapter or adaptor in genetic engineering is a short, chemically synthesized, double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. Double stranded adapters are different from linkers in that they contain one blunt end and one sticky end. For instance, a double stranded DNA adapter can be used to link the ends of two other DNA molecules (i.e., ends that do not have "sticky ends", that is complementary protruding single strands by themselves). It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently. Two adapters could base pair to each other to form dimers. Types of Adapters A conversion adapter is used to join a DNA insert cut with one restriction enzyme A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pacific Biosciences
Pacific Biosciences of California, Inc. (aka PacBio) is an American biotechnology company founded in 2004 that develops and manufactures systems for gene sequencing and some novel real time biological observation. PacBio has two principal sequencing platforms: single-molecule real-time sequencing (SMRT), based on the properties of zero-mode waveguides and sequencing by binding (SBB) chemistry, which uses native nucleotides and scarless incorporation for DNA binding and extension. History The company was founded based on research done at Cornell University that combined semiconductor processing and photonics with biotechnology research. Three graduate students in the lab of Professors Watt W. Webb — Jonas Korlach — and Harold Craighead — Steve Turner and Mathieu Foquet — became the first employees. It began under the name Nanofluidics, Inc. The company raised nearly in six rounds of primarily venture capital financing, making it one of the most cap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sanger Sequencing
Sanger sequencing is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Frederick Sanger and colleagues in 1977, it became the most widely used sequencing method for approximately 40 years. An automated instrument using slab gel electrophoresis and fluorescent labels was first commercialized by Applied Biosystems in March 1987. Later, automated slab gels were replaced with automated capillary array electrophoresis. Recently, higher volume Sanger sequencing has been replaced by next generation sequencing methods, especially for large-scale, automated genome analyses. However, the Sanger method remains in wide use for smaller-scale projects and for validation of deep sequencing results. It still has the advantage over short-read sequencing technologies (like Illumina) in that it can produce DNA sequence reads of > ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maxam–Gilbert Sequencing
Maxam–Gilbert sequencing is a method of DNA sequencing developed by Allan Maxam and Walter Gilbert in 1976–1977. This method is based on nucleobase-specific partial chemical modification of DNA and subsequent cleavage of the DNA backbone at sites adjacent to the modified nucleotides. Maxam–Gilbert sequencing was the first widely adopted method for DNA sequencing, and, along with the Sanger dideoxy method, represents the first generation of DNA sequencing methods. Maxam–Gilbert sequencing is no longer in widespread use, having been supplanted by next-generation sequencing methods. History Although Maxam and Gilbert published their chemical sequencing method two years after Frederick Sanger and Alan Coulson published their work on plus-minus sequencing, Maxam–Gilbert sequencing rapidly became more popular, since purified DNA could be used directly, while the initial Sanger method required that each read start be cloned for production of single-stranded DNA. However, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Massive Parallel Sequencing
Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged between 1993 and 1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads (50 to 400 bases each) per instrument run. Many NGS platforms differ in engineering configurations and sequencing chemistry. They share the technical paradigm of massive parallel sequencing via spatially separated, clonally amplified DNA templates or single DNA molecules in a flow cell. This design is very different from that of Sanger sequencing—also known as capillary sequencing or first-generation sequencing—which is based on electrophoretic separation of chain-termination products produced in ind ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Third-generation Sequencing
Third-generation sequencing (also known as long-read sequencing) is a class of DNA sequencing methods that have the capability to produce substantially longer reads (ranging from 10 kb to >1 Mb in length) than second generation sequencing, also known as next-generation sequencing methods. These methods emerged in 2008, characterized by technologies such as nanopore sequencing or single-molecule real-time sequencing, and continue to be developed. The ability to sequence longer reads has critical implications for both genome science and the study of biology in general. In structural variant calling, third generation sequencing has been found to outperform existing methods, even at a low depth of sequencing coverage. However, third generation sequencing data have much higher error rates than previous technologies, which can complicate downstream genome assembly and analysis of the resulting data. These technologies are undergoing active development and it is expected that there will ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reference Genome
A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the genome, set of genes in one idealized individual organism of a species. As they are assembled from the sequencing of DNA from a number of individual donors, reference genomes do not accurately represent the set of genes of any single individual organism. Instead, a reference provides a haploid mosaic of different DNA sequences from each donor. For example, one of the most recent human reference genomes, assembly ''GRCh38, GRCh38/hg38'', is derived from >60 genomic library, genomic clone libraries. There are reference genomes for multiple species of viruses, bacteria, fungus, plants, and animals. Reference genomes are typically used as a guide on which new genomes are built, enabling them to be assembled much more quickly and cheaply than the initial Human Genome Project. Reference genomes can be accessed online at several ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Epigenetics
In biology, epigenetics is the study of changes in gene expression that happen without changes to the DNA sequence. The Greek prefix ''epi-'' (ἐπι- "over, outside of, around") in ''epigenetics'' implies features that are "on top of" or "in addition to" the traditional (DNA sequence based) genetic mechanism of inheritance. Epigenetics usually involves a change that is not erased by cell division, and affects the regulation of gene expression. Such effects on cellular and physiological traits may result from environmental factors, or be part of normal development. The term also refers to the mechanism of changes: functionally relevant alterations to the genome that do not involve mutation of the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. Further, non-coding RNA sequences have been shown to play a key role in the r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
