A contig is a set of overlapping DNA segments that together represent a consensus region of DNA. In bottom-up sequencing projects, a contig refers to overlapping sequence data. Contigs can thus refer both to overlapping DNA sequence and to overlapping physical segments contained in clones depending on the context. In 1980, Staden wrote: In order to make it easier to talk about our data gained by the shotgun method of sequencing we have invented the word "contig". A contig is a set of gel readings. All gel readings belong to one and only one contig, each contig contains at least one gel reading; the gel readings in a contig can be summed to form a contiguous consensus sequence and the length of this sequence is the length of the contig. A sequence contig is a continuous sequence resulting from the reassembly of the small DNA fragments generated by bottom-up sequencing strategies; this meaning of contig is consistent with the original definition by Rodger Staden. The bottom-up DNA sequencing strategy involves shearing genomic DNA into many small fragments, sequencing these fragments, reassembling them back into contigs and the entire genome.
Because current technology allows for the direct sequencing of only short DNA fragments, genomic DNA must be fragmented into small pieces prior to sequencing. In bottom-up sequencing projects, amplified DNA is sheared randomly into fragments appropriately sized for sequencing; the subsequent sequence reads, which are the data that contain the sequences of the small fragments, are put into a database. The assembly software searches this database for pairs of overlapping reads. Assembling the reads from such a pair produces a longer contiguous read of sequenced DNA. By repeating this process many times, at first with the initial short pairs of reads but using longer pairs that are the result of previous assembly, the DNA sequence of an entire chromosome can be determined. Today, it is common to use paired-end sequencing technology where both ends of sized longer DNA fragments are sequenced. Here, a contig still refers to any contiguous stretch of sequence data created by read overlap; because the fragments are of known length, the distance between the two end reads from each fragment is known.
This gives additional information about the orientation of contigs constructed from these reads and allows for their assembly into scaffolds. Scaffolds consist of overlapping contigs separated by gaps of known length; the new constraints placed on the orientation of the contigs allows for the placement of repeated sequences in the genome. If one end read has a repetitive sequence, as long as its mate pair is located within a contig, its placement is known; the remaining gaps between the contigs in the scaffolds can be sequenced by a variety of methods, including PCR amplification followed by sequencing and BAC cloning methods followed by sequencing for larger gaps. Contig can refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical sequencing strategy is used. In this sequencing method, a low-resolution map is made prior to sequencing in order to provide a framework to guide the assembly of the sequence reads of the genome; this map identifies the relative overlap of the clones used for sequencing.
Sets of overlapping clones that form a contiguous stretch of DNA are called contigs. Once a tiling path has been selected, its component BACs are sheared into smaller fragments and sequenced. Contigs therefore provide the framework for hierarchical sequencing; the assembly of a contig map involves several steps. First, DNA is sheared into larger pieces, which are cloned into PACs to form a BAC library. Since these clones should cover the entire genome/chromosome, it is theoretically possible to assemble a contig of BACs that covers the entire chromosome. Reality, however, is not always ideal. Gaps remain, a scaffold—consisting of contigs and gaps—that covers the map region is the first result; the gaps between contigs can be closed by various methods outlined below. BAC contigs are constructed by aligning BAC regions of known overlap via a variety of methods. One common strategy is to use sequence-tagged site content mapping to detect unique DNA sites in common between BACs; the degree of overlap is estimated by the number of STS markers in common between two clones, with more markers in common signifying a greater overlap.
Because this strategy provides only a rough estimate of overlap, restriction digest fragment analysis, which provides a more precise measurement of clone overlap, is used. In this strategy, clones are treated with one or two restriction enzymes and the resulting fragments separated by gel electrophoresis. If two clones, they will have restriction sites in common, will thus share several fragments; because the number of fragments in common and the length of these fragments is known, the degree of overlap can be deduced to a high degree of precision. Gaps remain after initial BAC contig construction; these gaps occur if the Bacterial Artificial Chromosome library screened has low complexity, meaning it does not con
Human Genome Project
The Human Genome Project was an international scientific research project with the goal of determining the sequence of nucleotide base pairs that make up human DNA, of identifying and mapping all of the genes of the human genome from both a physical and a functional standpoint. It remains the world's largest collaborative biological project. After the idea was picked up in 1984 by the US government when the planning started, the project formally launched in 1990 and was declared complete on April 14, 2003. Funding came from the US government through the National Institutes of Health as well as numerous other groups from around the world. A parallel project was conducted outside government by the Celera Corporation, or Celera Genomics, formally launched in 1998. Most of the government-sponsored sequencing was performed in twenty universities and research centers in the United States, the United Kingdom, France and China; the Human Genome Project aimed to map the nucleotides contained in a human haploid reference genome.
The "genome" of any given individual is unique. Therefore, the finished human genome is a mosaic; the Human Genome Project was a 15-year-long, publicly funded project initiated in 1990 with the objective of determining the DNA sequence of the entire euchromatic human genome within 15 years. In May 1985, Robert Sinsheimer organized a workshop to discuss sequencing the human genome, but for a number of reasons the NIH was uninterested in pursuing the proposal; the following March, the Santa Fe Workshop was organized by Charles DeLisi and David Smith of the Department of Energy's Office of Health and Environmental Research. At the same time Renato Dulbecco proposed whole genome sequencing in an essay in Science. James Watson followed two months with a workshop held at the Cold Spring Harbor Laboratory; the fact that the Santa Fe workshop was motivated and supported by a Federal Agency opened a path, albeit a difficult and tortuous one, for converting the idea into a public policy in the United States.
In a memo to the Assistant Secretary for Energy Research, Charles DeLisi, Director of the OHER, outlined a broad plan for the project. This started a long and complex chain of events which led to approved reprogramming of funds that enabled the OHER to launch the Project in 1986, to recommend the first line item for the HGP, in President Reagan's 1988 budget submission, approved by the Congress. Of particular importance in Congressional approval was the advocacy of Senator Peter Domenici, whom DeLisi had befriended. Domenici chaired the Senate Committee on Energy and Natural Resources, as well as the Budget Committee, both of which were key in the DOE budget process. Congress added a comparable amount to the NIH budget, thereby beginning official funding by both agencies. Alvin Trivelpiece sought and obtained the approval of DeLisi's proposal by Deputy Secretary William Flynn Martin; this chart was used in the spring of 1986 by Trivelpiece Director of the Office of Energy Research in the Department of Energy, to brief Martin and Under Secretary Joseph Salgado regarding his intention to reprogram $4 million to initiate the project with the approval of Secretary Herrington.
This reprogramming was followed by a line item budget of $16 million in the Reagan Administration’s 1987 budget submission to Congress. It subsequently passed both Houses; the Project was planned for 15 years. Candidate technologies were being considered for the proposed undertaking at least as early as 1985. In 1990, the two major funding agencies, DOE and NIH, developed a memorandum of understanding in order to coordinate plans and set the clock for the initiation of the Project to 1990. At that time, David Galas was Director of the renamed “Office of Biological and Environmental Research” in the U. S. Department of Energy's Office of Science and James Watson headed the NIH Genome Program. In 1993, Aristides Patrinos succeeded Galas and Francis Collins succeeded James Watson, assuming the role of overall Project Head as Director of the U. S. National Institutes of Health National Center for Human Genome Research. A working draft of the genome was announced in 2000 and the papers describing it were published in February 2001.
A more complete draft was published in 2003, genome "finishing" work continued for more than a decade. The $3-billion project was formally founded in 1990 by the US Department of Energy and the National Institutes of Health, was expected to take 15 years. In addition to the United States, the international consortium comprised geneticists in the United Kingdom, Australia and myriad other spontaneous relationships. Considering the inflation, the project costed $5 billion. Due to widespread international cooperation and advances in the field of genomics, as well as major advances in computing technology, a'rough draft' of the genome was finished in 2000; this first available rough draft assembly of the genome was completed by the Genome Bioinformatics Group at the University of California, Santa Cruz led by graduate student Jim Kent. Ongoing sequencing led to the announcement of the complete genome on April 14, 2003, two years earlier than planned. In May 2006, another milestone was passed on the way to completion of the project, when the sequence of
Drosophila melanogaster is a species of fly in the family Drosophilidae. The species is known as the common fruit fly or vinegar fly. Starting with Charles W. Woodworth's proposal of the use of this species as a model organism, D. melanogaster continues to be used for biological research in genetics, microbial pathogenesis, life history evolution. As of 2017, eight Nobel prizes had been awarded for research using Drosophila. D. Melanogaster is used in research because it can be reared in the laboratory, has only four pairs of chromosomes and lays many eggs, its geographic range includes all continents, including islands. D. melanogaster is a common pest in homes and other places where food is served. Flies belonging to the family Tephritidae are called "fruit flies"; this can cause confusion in the Mediterranean and South Africa, where the Mediterranean fruit fly Ceratitis capitata is an economic pest. Wildtype fruit flies are yellow-brown, with brick-red eyes and transverse black rings across the abdomen.
They exhibit sexual dimorphism. Males are distinguished from females based on colour differences, with a distinct black patch at the abdomen, less noticeable in emerged flies, the sexcombs. Furthermore, males have a cluster of spiky hairs surrounding the reproducing parts used to attach to the female during mating. Extensive images are found at FlyBase. Under optimal growth conditions at 25 °C, the D. melanogaster lifespan is about 50 days from egg to death. The developmental period for D. melanogaster varies with temperature, as with many ectothermic species. The shortest development time, 7 days, is achieved at 28 °C. Development times increase at higher temperatures due to heat stress. Under ideal conditions, the development time at 25 °C is 8.5 days, at 18 °C it takes 19 days and at 12 °C it takes over 50 days. Under crowded conditions, development time increases. Females lay some 400 eggs, about five at a time, into rotting fruit or other suitable material such as decaying mushrooms and sap fluxes.
The eggs, which are about 0.5 mm long, hatch after 12–15 hours. The resulting larvae grow for about 4 days while molting twice, at about 48 h after hatching. During this time, they feed on the microorganisms that decompose the fruit, as well as on the sugar of the fruit itself; the mother puts feces on the egg sacs to establish the same microbial composition in the larvae's guts that has worked positively for herself. The larvae encapsulate in the puparium and undergo a 4-day-long metamorphosis, after which the adults eclose; the female fruit fly prefers a shorter duration. Males, prefer it to last longer. Males perform a sequence of five behavioral patterns to court females. First, males orient themselves while playing a courtship song by horizontally extending and vibrating their wings. Soon after, the male positions himself at the rear of the female's abdomen in a low posture to tap and lick the female genitalia; the male curls his abdomen and attempts copulation. Females can reject males by moving away and extruding their ovipositor.
Copulation lasts around 15–20 minutes, during which males transfer a few hundred long sperm cells in seminal fluid to the female. Females store the sperm in two mushroom-shaped spermathecae. A last male precedence is believed to exist; this precedence was found to occur through both incapacitation. The displacement is attributed to sperm handling by the female fly as multiple matings are conducted and is most significant during the first 1–2 days after copulation. Displacement from the seminal receptacle is more significant than displacement from the spermathecae. Incapacitation of first male sperm by second male sperm becomes significant 2–7 days after copulation; the seminal fluid of the second male is believed to be responsible for this incapacitation mechanism which takes effect before fertilization occurs. The delay in effectiveness of the incapacitation mechanism is believed to be a protective mechanism that prevents a male fly from incapacitating his own sperm should he mate with the same female fly repetitively.
Sensory neurons in the uterus of female D. melanogaster respond to a male protein, sex peptide, found in sperm. This protein makes the female reluctant to copulate for about 10 days after insemination; the signal pathway leading to this change in behavior has been determined. The signal is sent to a brain region, a homolog of the hypothalamus and the hypothalamus controls sexual behavior and desire. Gonadotropic hormones in Drosophila maintain homeostasis and govern reproductive output via a cyclic interrelationship, not unlike the mammalian estrous cycle. Sex Peptide perturbs this homeostasis and shifts the endocrine state of the female by inciting juvenile hormone synthesis in the corpus allatum. D. Melanogaster is used for life extension studies, such as to identify genes purported to increase lifespan when mutated. Females become receptive to courting males about 8–12 hours after emergence. Specific neuron groups in females have been found to affect copulation behavior a
In genetics and biochemistry, sequencing means to determine the primary structure of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. So far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger; this technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as pyrosequencing are gaining an increasing share of the sequencing market. More genome data are now being produced by pyrosequencing than Sanger DNA sequencing. Pyrosequencing has enabled rapid genome sequencing. Bacterial genomes can be sequenced in a single run with several times coverage with this technique; this technique was used to sequence the genome of James Watson recently.
The sequence of DNA encodes the necessary information for living things to reproduce. Determining the sequence is therefore useful in fundamental research into why and how organisms live, as well as in applied subjects; because of the key importance DNA has to living things, knowledge of DNA sequences is useful in any area of biological research. For example, in medicine it can be used to identify and develop treatments for genetic diseases. Research into pathogens may lead to treatments for contagious diseases. Biotechnology is a burgeoning discipline, with the potential for services; the Carlson curve is a term coined by The Economist to describe the biotechnological equivalent of Moore's law, is named after author Rob Carlson. Carlson predicted the doubling time of DNA sequencing technologies would be at least as fast as Moore's law. Carlson curves illustrate the rapid decreases in cost, increases in performance, of a variety of technologies, including DNA sequencing, DNA synthesis, a range of physical and computational tools used in protein expression and in determining protein structures.
In chain terminator sequencing, extension is initiated at a specific site on the template DNA by using a short oligonucleotide'primer' complementary to the template at that region. The oligonucleotide primer is extended using a DNA polymerase, an enzyme that replicates DNA. Included with the primer and DNA polymerase are the four deoxynucleotide bases, along with a low concentration of a chain terminating nucleotide. Limited incorporation of the chain terminating nucleotide by the DNA polymerase results in a series of related DNA fragments that are terminated only at positions where that particular nucleotide is used; the fragments are size-separated by electrophoresis in a slab polyacrylamide gel, or more now, in a narrow glass tube filled with a viscous polymer. An alternative to the labelling of the primer is to label the terminators instead called'dye terminator sequencing'; the major advantage of this approach is the complete sequencing set can be performed in a single reaction, rather than the four needed with the labeled-primer approach.
This is accomplished by labelling each of the dideoxynucleotide chain-terminators with a separate fluorescent dye, which fluoresces at a different wavelength. This method is easier and quicker than the dye primer approach, but may produce more uneven data peaks, due to a template dependent difference in the incorporation of the large dye chain-terminators; this problem has been reduced with the introduction of new enzymes and dyes that minimize incorporation variability. This method is now used for the vast majority of sequencing reactions as it is both simpler and cheaper; the major reason for this is that the primers do not have to be separately labelled, although this is less of a concern with used'universal' primers. This is changing due to the increasing cost-effectiveness of second- and third-generation systems from Illumina, 454, ABI, Dover. Pyrosequencing, developed by Pål Nyrén and Mostafa Ronaghi DNA, has been commercialized by Biotage and 454 Life Sciences; the latter platform sequences 100 megabases in a seven-hour run with a single machine.
In the array-based method, single-stranded DNA is annealed to beads and amplified via EmPCR. These DNA-bound beads are placed into wells on a fiber-optic chip along with enzymes which produce light in the presence of ATP; when free nucleotides are washed over this chip, light is produced as ATP is generated when nucleotides join with their complementary base pairs. Addition of one nucleotide results in a reaction that generates a light signal, recorded by the CCD camera in the instrument; the signal strength is proportional to the number of nucleotides, for example, homopolymer stretches, incorporated in a single nucleotide flow. Whereas the methods above describe various sequencing methods, separate related terms are used when a large portion of a genome is sequenced. Several platforms were developed to perform whole genome sequencing. RNA is less stable in the cell, more prone to nuclease attack experimentally. A
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology, used to determine the order of the four bases: adenine, guanine and thymine; the advent of rapid DNA sequencing methods has accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, in numerous applied fields such as medical diagnosis, forensic biology and biological systematics; 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 and microbial species. The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography. Following the development of fluorescence-based sequencing methods with a DNA sequencer, DNA sequencing has become easier and orders of magnitude faster.
DNA sequencing may be used to determine the sequence of individual genes, larger genetic regions, full chromosomes, or entire genomes of any organism. DNA sequencing is the most efficient way to indirectly sequence RNA or proteins. In fact, DNA sequencing has become a key technology in many areas of biology and other sciences such as medicine and anthropology. Sequencing is used in molecular biology to study genomes and the proteins they encode. Information obtained using sequencing allows researchers to identify changes in genes, associations with diseases and phenotypes, identify potential drug targets. Since DNA is an informative macromolecule in terms of transmission from one generation to another, DNA sequencing is used in evolutionary biology to study how different organisms are related and how they evolved; the field of metagenomics involves identification of organisms present in a body of water, dirt, debris filtered from the air, or swab samples from organisms. Knowing which organisms are present in a particular environment is critical to research in ecology, epidemiology and other fields.
Sequencing enables researchers to determine which types of microbes may be present in a microbiome, for example. Medical technicians may sequence genes from patients to determine if there is risk of genetic diseases; this is a form of genetic testing. DNA sequencing may be used along with DNA profiling methods for forensic identification and paternity testing. DNA testing has evolved tremendously in the last few decades to link a DNA print to what is under investigation; the DNA patterns in fingerprint, hair follicles, etc. uniquely separate each living organism from another. Testing DNA is a technique which can detect specific genomes in a DNA strand to produce a unique and individualized pattern; every living organism created has a one of a kind DNA pattern, which can be determined through DNA testing. It is rare that two people have the same DNA pattern, therefore DNA testing is successful; the canonical structure of DNA has four bases: thymine, adenine and guanine. DNA sequencing is the determination of the physical order of these bases in a molecule of DNA.
However, there are many other bases. In some viruses, cytosine may be replaced by hydroxy methyl glucose cytosine. In mammalian DNA, variant bases with methyl groups or phosphosulfate may be found. Depending on the sequencing technique, a particular modification, e.g. the 5mC common in humans, may or may not be detected. Deoxyribonucleic acid was first discovered and isolated by Friedrich Miescher in 1869, but it remained understudied for many decades because proteins, rather than DNA, were thought to hold the genetic blueprint to life; this situation changed after 1944 as a result of some experiments by Oswald Avery, Colin MacLeod, Maclyn McCarty demonstrating that purified DNA could change one strain of bacteria into another. This was the first time. In 1953, James Watson and Francis Crick put forward their double-helix model of DNA, based on crystallized X-ray structures being studied by Rosalind Franklin – and without crediting her. According to the model, DNA is composed of two strands of nucleotides coiled around each other, linked together by hydrogen bonds and running in opposite directions.
Each strand is composed of four complementary nucleotides – adenine, cytosine and thymine – with an A on one strand always paired with T on the other, C always paired with G. They proposed such a structure allowed each strand to be used to reconstruct the other, an idea central to the passing on of hereditary information between generations; 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. This provided the first conclusive evidence that proteins were chemical entities with a specific molecular pattern rather than a random mixture of material suspended in fluid. Sanger's success in sequencing insulin electrified x-ray crystallographers, including Watson and Crick who by now were trying to understand how DNA directed the formation of proteins within a cell. Soon after attending a series of lectures given by Frederick Sanger in October 1954, Crick began to develo
A base pair is a unit 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 base pairs allow the DNA helix to maintain a regular helical structure, subtly dependent on its nucleotide sequence; the complementary nature of this based-paired structure provides a 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 RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes. Intramolecular base pairs can occur within single-stranded nucleic acids.
This is important in RNA molecules, where Watson–Crick base pairs permit the formation of short double-stranded helices, a wide variety of non-Watson–Crick interactions allow RNAs to fold into a vast range of specific three-dimensional structures. In addition, base-pairing between transfer RNA and messenger RNA forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code; the size of an individual gene or an organism's entire genome is measured in base pairs because DNA is double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands; the haploid human genome is estimated to be about 3.2 billion bases long and to contain 20,000–25,000 distinct protein-coding genes. A kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA; the total amount of related DNA base pairs on Earth is estimated at 5.0×1037 and weighs 50 billion tonnes.
In comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the chemical interaction. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high GC-content is more stable than DNA with low GC-content. But, contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly; the larger nucleobases and guanine, are members of a class of double-ringed chemical structures called purines. Purines are complementary only with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established. Purine-pyrimidine base-pairing of AT or GC or UA results in proper duplex structure; the only other purine-pyrimidine pairings would be AC and GT and UG. The GU pairing, with two hydrogen bonds, does occur often in RNA. Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a melting point, determined by the length of the molecules, the extent of mispairing, the GC content.
Higher GC content results in higher melting temperatures. On the converse, regions of a genome that need to separate — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must be taken into account when designing primers for PCR reactions; the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5' end to the 3' end. A base-paired DNA sequence: ATCGATTGAGCTCTAGCG TAGCTAACTCGAGATCGCThe corresponding RNA sequence, in which uracil is substituted for thymine in the RNA strand: AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors in DNA replication and DNA transcription; this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine but can base-pair to guanine in its enol form. Other chemicals, known as DNA intercalators, fit into the gap between adjacent bases on a single strand and induce frameshift mutations by "masquerading" as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site.
Most intercalators are known or suspected carcinogens. Examples include ethidium acridine. An unnatural base pair is a designed subunit of DNA, created in a laboratory and does not occur in nature. DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two ba
The human genome is the complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are treated separately as the nuclear genome, the mitochondrial genome. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells consist of three billion DNA base pairs, while diploid genomes have twice the DNA content. While there are significant differences among the genomes of human individuals, these are smaller than the differences between humans and their closest living relatives, the chimpanzees and bonobos; the first human genome sequences were published in nearly complete draft form in February 2001 by the Human Genome Project and Celera Corporation. Completion of the Human Genome Project Sequence was published in 2004; the human genome was the first of all vertebrates to be sequenced. As of 2012, thousands of human genomes have been sequenced, many more have been mapped at lower levels of resolution.
This data is used worldwide in biomedical science, anthropology and other branches of science. There is a held expectation that genomic studies will lead to advances in the diagnosis and treatment of diseases, to new insights in many fields of biology, including human evolution. Although the sequence of the human genome has been determined by DNA sequencing, it is not yet understood. Most genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products. Recent results suggest that most of the vast quantities of noncoding DNA within the genome have associated biochemical activities, including regulation of gene expression, organization of chromosome architecture, signals controlling epigenetic inheritance. There are an estimated 19,000-20,000 human protein-coding genes; the estimate of the number of human genes has been revised down from initial predictions of 100,000 or more as genome sequence quality and gene finding methods have improved, could continue to drop further.
Protein-coding sequences account for only a small fraction of the genome, the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, sequences for which as yet no function has been determined. In June 2016, scientists formally announced a plan to synthesize the human genome; the total length of the human genome is over 3 billion base pairs. The genome is organized into 22 paired chromosomes, plus the X chromosome and, in males only, one Y chromosome; these are all large linear DNA molecules contained within the cell nucleus. The genome includes the mitochondrial DNA, a comparatively small circular molecule present in each mitochondrion. Basic information about these molecules and their gene content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table. Table 1 summarizes the physical organization and gene content of the human reference genome, with links to the original analysis, as published in the Ensembl database at the European Bioinformatics Institute and Wellcome Trust Sanger Institute.
Chromosome lengths were estimated by multiplying the number of base pairs by 0.34 nanometers, the distance between base pairs in the DNA double helix. The number of proteins is based on the number of initial precursor mRNA transcripts, does not include products of alternative pre-mRNA splicing, or modifications to protein structure that occur after translation. Variations are unique DNA sequence differences that have been identified in the individual human genome sequences analyzed by Ensembl as of December, 2016; the number of identified variations is expected to increase as further personal genomes are sequenced and analyzed. In addition to the gene content shown in this table, a large number of non-expressed functional sequences have been identified throughout the human genome. Links open windows to the reference chromosome sequences in the EBI genome browser. Small non-coding RNAs are RNAs of as many as 200 bases; these include: microRNAs, or miRNAs, small nuclear RNAs, or snRNAs, small nucleolar RNAs, or snoRNA.
Long non-coding RNAs are RNA molecules longer than 200 bases that do not have protein-coding potential. These include: ribosomal RNAs, or rRNAs, a variety of other long RNAs that are involved in regulation of gene expression, epigenetic modifications of DNA nucleotides and histone proteins, regulation of the activity of protein-coding genes. Small discrepancies between total-small-ncRNA numbers and the numbers of specific types of small ncNRAs result from the former values being sourced from Ensembl release 87 and the latter from Ensembl release 68. Although the human genome has been sequenced for all practical purposes, there are still hundreds of gaps in the sequence. A recent study noted more than 160 euchromat