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Encyclopedia > Genome project

Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus). The genome sequence for any organism requires the DNA sequences for each of the chromosomes in an organism to be determined. For bacteria, which usually have just one chromosome, a genome project will aim to map the sequence of that chromosome. Humans, with 22 pairs of chromosomes and 2 sex chromosomes, will require 24 separate chromosome sequences in order to represent the completed genome. For the scientific journal named Science, see Science (journal). ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... “Life on Earth” redirects here. ... For other uses, see Animal (disambiguation). ... For other uses, see Plant (disambiguation). ... Subkingdom/Phyla Chytridiomycota Blastocladiomycota Neocallimastigomycota Glomeromycota Zygomycota Dikarya (inc. ... Phyla/Divisions Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Omnibacteria Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular, bacterium) are a major group of living organisms. ... The Archean is a geologic eon; it is a somewhat antiquated term for the time span between 2500 million years before the present and 3800 million years before the present. ... Typical phyla Chromalveolata Chromista Heterokontophyta Haptophyta Cryptophyta (cryptomonads) Alveolata Dinoflagellata Apicomplexa Ciliophora (ciliates) Cabozoa Excavata Euglenozoa Percolozoa Metamonada Rhizaria Radiolaria Foraminifera Cercozoa Archaeplastida (in part) Rhodophyta (red algae) Glaucophyta (basal archaeplastids) Amoebozoa Choanozoa Many others; classification varies Protists (IPA: (RP); (GenAm)), Greek protiston -a meaning the (most) first of all... This article is about biological infectious particles. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... This article is about the biological chromosome. ... Phyla Actinobacteria Aquificae Chlamydiae Bacteroidetes/Chlorobi Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia Bacteria (singular: bacterium) are unicellular microorganisms. ...


The Human Genome Project was a landmark genome project and some have argued that the era of genomics is one of the more fundamental advances in human history. The Human Genome Project (HGP) is a project undertaken with a goal to understand the genetic make-up of the human species by identifying all the genes in the human genome and mapping how individual genes are sequenced. ... Genomics is the study of an organisms entire genome; Rathore et al, . Investigation of single genes, their functions and roles is something very common in todays medical and biological research, and cannot be said to be genomics but rather the most typical feature of molecular biology. ...

Contents

Genome assembly

Genome assembly refers to the process of taking a large number of short DNA sequences, all of which were generated by a shotgun sequencing project, and putting them back together to create a representation of the original chromosomes from which the DNA originated. In a shotgun sequencing project, all the DNA from a source (usually a single organism, anything from a bacterium to a mammal) is first fractured into millions of small pieces. These pieces are then "read" by automated sequencing machines, which can read up to 900 nucleotides or bases at a time. (The four bases are adenine, guanine, cytosine, and thymine, represented as AGCT.) A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads, overlap. These overlapping reads can be merged together, and the process continues. part of a DNA sequence A DNA sequence (sometimes genetic sequence) is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand (adenine, cytosine, guanine... Shotgun sequencing is a method used in genetics for sequencing long DNA strands. ... Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... “Life on Earth” redirects here. ... Phyla/Divisions Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Omnibacteria Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular, bacterium) are a major group of living organisms. ... Subclasses & Infraclasses Subclass †Allotheria* Subclass Prototheria Subclass Theria Infraclass †Trituberculata Infraclass Metatheria Infraclass Eutheria Mammals (class Mammalia) are warm-blooded, vertebrate animals characterized by the production of milk in female mammary glands and by the presence of: hair, three middle ear bones used in hearing, and a neocortex region in... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... This article or section does not adequately cite its references or sources. ... Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA; the others being adenine, cytosine, thymine, and uracil. ... Cytosine is one of the 5 main nucleobases used in storing and transporting genetic information within a cell in the nucleic acids DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at... For the similarly-spelled vitamin compound, see Thiamine Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... In mathematics, computing, linguistics, and related disciplines, an algorithm is a finite list of well-defined instructions for accomplishing some task that, given an initial state, will terminate in a defined end-state. ...


Genome assembly is a very difficult computational problem, made more difficult because genomes contain large numbers of identical sequences, known as repeats. These repeats can be thousands of nucleotides long, and some occur in thousands of different locations, especially in the large genomes of plants and animals. The tower of a personal computer. ... For other uses, see Plant (disambiguation). ... For other uses, see Animal (disambiguation). ...


Assembly software

Most research institutes that sequence DNA use their own software for assembling the sequences that they produce. Some well known assembly programs include:


Phred/Phrap by Phil Green


AMOS (A Modular, Open-Source assembler) is a well-known open source effort to bring together the efforts of leading genome assembly code developers. The home of AMOS is currently http://amos.sourceforge.net. AMOS was initiated at The Institute for Genomic Research by Steven Salzberg, Mihai Pop, and Art Delcher. Open source refers to projects that are open to the public and which draw on other projects that are freely available to the general public. ... The Institute for Genomic Research (TIGR), is a non-profit genomics research institute founded in 1992 by Craig Venter in Rockville, Maryland, United States. ...


The Celera Assembler was the assembler developed by Gene Myers, Granger Sutton, Art Delcher, and others at Celera Genomics from 1998 until approximately 2002. It was moved to SourceForge and continues to be developed by the original scientists and others, at http://sourceforge.net/projects/wgs-assembler. Gene Myers is a professor of computer science at the University of California, Berkeley, whose research focuses on algorithms and computational biology. ... Celera Genomics (NYSE: CRA) is a business unit of the Applera Corporation that focuses on genetic sequencing and related technologies. ... SourceForge is a collaborative revision control and software development management system. ...


The Arachne assembler began in 2000 as the doctoral thesis of Serafim Batzoglou, now at Stanford University. Since that time, it has been developed by a team lead by David B. Jaffe at the Broad Institute, formerly part of the Whitehead Institute. It is available for download at http://www.broad.mit.edu/wga/. “Stanford” redirects here. ... The Broad Institute of MIT and Harvard, formerly the Whitehead Institute/MIT Center for Genome Research (WICGR), is a multidisciplinary institution dedicated to fulfilling the potential of genomics for the biomedical sciences. ... Founded in 1984, the Whitehead Institute for Biomedical Research is a non-profit research and teaching institution located in Cambridge, Massachusetts. ...


Genome annotation

Genome annotation is the process of attaching biological information to sequences. It consists of two main steps: part of a DNA sequence A DNA sequence (sometimes genetic sequence) is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand (adenine, cytosine, guanine...

  1. identifying elements on the genome, a process called Gene Finding, and
  2. attaching biological information to these elements.

Automatic annotation tools try to perform all this by computer analysis, as opposed to manual annotation which involves human expertise. Ideally, these approaches co-exist and complement each other in the same annotation pipeline. In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Gene finding is the area of computational biology that is concerned with algorithmically identifying stretches of sequence, usually genomic DNA, that are biologically functional. ...


The basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on that. However, nowadays more and more additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. ...


For example, the SEED database uses genome context information, similarity scores, experimental data, and integrations of other resources to provide the most accurate genome annotations through their Subsystems approach.


Structural annotation consists in the identification of genomic elements.

  • ORFs and their localisation
  • gene structure
  • coding regions
  • location of regulatory motifs

Functional annotation consists in attaching biological information to genomic elements.

  • biochemical function
  • biological function
  • involved regulation and interactions
  • expression

These steps may involve both biological experiments and in silico analysis.


A variety of software tools have been developed to permit scientists to view and share genome annotations.


When is a genome project finished?

When sequencing a genome, there are usually regions that are difficult to sequence (often regions with highly repetitive DNA). Thus, 'completed' genome sequences are rarely ever complete, and terms such as 'working draft' or 'essentially complete' have been used to more accurately describe the status of such genome projects. Even when every base pair of a genome sequence has been determined, there are still likely to be errors present because DNA sequencing is not a completely accurate process. It could also be argued that a complete genome project should include the sequences of mitochondria and (for plants) chloroplasts as these organelles have their own genomes. In genetics and biochemistry, sequencing means to determine the primary structure (or primary sequence) of an unbranched biopolymer. ... In the study of DNA sequences, one can distinguish two main types of repeated sequence: Tandem repeats: Satellite DNA, Minisatellite, Microsatellite; Interspersed repeats: SINE (Short INterspersed Elements), LINE (Long INterspersed Elements). ... Base pairs, of a DNA molecule. ... In cell biology, a mitochondrion is an organelle found in the cells of most eukaryotes. ... Chloroplasts are organelles found in plant cells and eukaryotic algae which conduct photosynthesis. ... In cell biology, an organelle is one of several structures with specialized functions, suspended in the cytoplasm of a eukaryotic cell. ...


It is often reported that the goal of sequencing a genome is to obtain information about the complete set of genes in that particular genome sequence. The proportion of a genome that encodes for genes may be very small (particularly in eukaryotes such as humans, where coding DNA may only account for a few percent of the entire sequence). However, it is not always possible (or desirable) to only sequence the coding regions separately. Also, as scientists understand more about the role of this noncoding DNA (often referred to as junk DNA), it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism. This stylistic schematic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). ... Kingdoms Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound nuclei. ... The coding region of a gene is the portion of DNA that is transcribed into mRNA and translated into proteins. ... The coding region of a gene is the portion of DNA that is transcribed into mRNA and translated into proteins. ... It has been suggested that junk DNA be merged into this article or section. ... In molecular biology, junk DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. ...


In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism. Such projects may also include gene prediction to find out where the genes are in a genome, and what those genes do. There may also be related projects to sequence ESTs or mRNAs to help find out where the genes actually are. 7Gene finding typically refers to the area of computational biology that is concerned with algorithmically identifying stretches of sequence, usually genomic DNA, that are biologically functional. ... An expressed sequence tag or EST is a short sub-sequence of a transcribed spliced nucleotide sequence (either protein-coding or not). ... The interaction of mRNA in a eukaryote cell. ...


Historical and Technological Perspectives

Historically, when sequencing eukaryotic genomes (such as the worm Caenorhabditis elegans) it was common to first map the genome to provide a series of landmarks across the genome. Rather than sequence a chromosome in one go, it would be sequenced piece by piece (with the prior knowledge of approximately where that piece is located on the larger chromosome). Changes in technology and in particular improvements to the processing power of computers, means that genomes can now be 'shotgun sequenced' in one go (there are caveats to this approach though when compared to the traditional approach). Binomial name Maupas, 1900 Caenorhabditis elegans (IPA: ) is a free-living nematode (roundworm), about 1 mm in length, which lives in temperate soil environments. ... A genetic map refers to the assignment of DNA fragments to chromosomes. ... Whole genome shotgun sequencing is a semi-automated technique for shotgun sequencing DNA, in which high-molecular-weight DNA is sheared into random fragments, size selected (usually 2, 10, 50, and 150 kb), and cloned into an appropriate vector. ...


Improvements in DNA sequencing technology has meant that the cost of sequencing a new genome sequence has steadily fallen (in terms of cost per base pair) and newer technology has also meant that genomes can be sequenced far more quickly. When research agencies decide what new genomes to sequence, the emphasis has been on species which have either a relevance to human health (e.g. pathogenic bacteria or vectors of disease such as mosquitos) or species which have commercial importance (e.g. livestock and crop plants). Secondary emphasis is placed on species whose genomes will help answer important questions in molecular evolution (e.g. the common chimpanzee). The term DNA sequencing encompasses biochemical methods for determining the order of the nucleotide bases, adenine, guanine, cytosine, and thymine, in a DNA oligonucleotide. ... Base pairs, of a DNA molecule. ... Phyla Actinobacteria Aquificae Chlamydiae Bacteroidetes/Chlorobi Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia Bacteria (singular: bacterium) are unicellular microorganisms. ... In epidemiology, a vector is an organism that does not cause disease itself but which spreads infection by conveying pathogens from one host to another. ... For other uses, see Mosquito (disambiguation). ... Type species Simia troglodytes Blumenbach, 1775 distribution of Species Pan troglodytes Pan paniscus Chimpanzee, often shortened to chimp, is the common name for the two extant species in the genus Pan. ...


In the future, it is likely that it will become even cheaper and quicker to sequence a genome. This will allow for complete genome sequences to be determined from many different individuals of the same species. For humans, this will allow us to better understand aspects of human genetic diversity. The Human Genome Diversity Project (HGDP) was started by Stanford Universitys Morrison Institute and a collaboration of scientists around the world. ...


Example genome projects

The common fruit fly, one of the first higher organisms to have its genome completely sequenced.
The common fruit fly, one of the first higher organisms to have its genome completely sequenced.
The zebrafish, another important model organism in genomics.
The zebrafish, another important model organism in genomics.
The International Grape Genome Program aims to improve control, yield and quality in wine grape production.

Many organisms have genome projects that have either been completed or will be completed shortly, including: Image File history File links File links The following pages link to this file: Drosophila melanogaster ... Image File history File links File links The following pages link to this file: Drosophila melanogaster ... Binomial name Meigen, 1830[1] Drosophila melanogaster (from the Greek for black-bellied dew-lover) is a two-winged insect that belongs to the Diptera, the order of the flies. ... Image File history File linksMetadata Download high-resolution version (820x392, 98 KB) A w:en:Zebrafish (w:en:Zebra Danio). ... Image File history File linksMetadata Download high-resolution version (820x392, 98 KB) A w:en:Zebrafish (w:en:Zebra Danio). ... Binomial name Danio rerio (Hamilton-Buchanan, 1822) The Zebra Danio or Zebrafish (Brachydanio rerio or Danio rerio) is a tropical fish, commonly kept in aquaria and used for scientific research, belonging to the minnow family (Cyprinidae). ... Genomics is the study of an organisms entire genome; Rathore et al, . Investigation of single genes, their functions and roles is something very common in todays medical and biological research, and cannot be said to be genomics but rather the most typical feature of molecular biology. ... Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ...

This article is about modern humans. ... The Human Genome Project (HGP) is a project undertaken with a goal to understand the genetic make-up of the human species by identifying all the genes in the human genome and mapping how individual genes are sequenced. ... For other uses, see Neanderthal (disambiguation). ... Binomial name Haemophilus influenzae (Lehmann & Neumann 1896) Winslow 1917 Haemophilus influenzae, formerly called Pfeiffers bacillus or Bacillus influenzae, is a non-motile Gram-negative coccobacillus first described in 1892 by Dr. Richard Pfeiffer during an influenza pandemic. ... Binomial name Mus musculus Linnaeus, 1758 Mus musculus is the common house mouse. ... Binomial name (Berkenhout, 1769) Brown Rat range The brown rat, common rat, Norway rat, Norwegian rat or wharf rat (Rattus norvegicus) is one of the best-known and common rats, and also one of the largest. ... Binomial name (Blumenbach, 1775) distribution of Common Chimpanzee. ... The Chimpanzee Genome Project is an effort to determine the DNA sequence of the genome of the closest living human relatives. ... Binomial name Macaca mulatta (Zimmermann, 1780) The Rhesus Macaque (Macaca mulatta), often called the Rhesus Monkey, is one of the best known species of Old World monkeys. ... This article or section does not adequately cite its references or sources. ... Binomial name Macropus eugenii The Tammar Wallaby (Macropus eugenii) is a small member of the kangaroo family and is the type species for research on kangaroos and marsupials. ... Binomial name Felis catus Linnaeus, 1758 Synonyms Felis lybica invalid junior synonym The cat (or domestic cat, house cat) is a small carnivorous mammal. ... Trinomial name Canis lupus familiaris The dog (Canis lupus familiaris) is a domestic subspecies of the wolf, a mammal of the Canidae family of the order Carnivora. ... Binomial name Meigen, 1830[1] Drosophila melanogaster (from the Greek for black-bellied dew-lover) is a two-winged insect that belongs to the Diptera, the order of the flies. ... Binomial name Meyen ex E.C. Hansen Saccharomyces cerevisiae is a species of budding yeast. ... Binomial name Neurospora crassa Shear & B.O. Dodge Neurospora crassa is a type of red bread mold of the phylum Ascomycota. ... Binomial name Arabidopsis thaliana (L.) Heynh. ... For other uses, see Rice (disambiguation). ... Species T. aestivum T. boeoticum T. compactum T. dicoccoides T. dicoccon T. durum T. monococcum T. spelta T. sphaerococcum T. timopheevii References:   ITIS 42236 2002-09-22 For the indie rock group see: Wheat (band). ... This article is about the maize plant. ... This article is about woody plants of the genus Populus. ... Binomial name Populus trichocarpa (Torr. ... E. coli redirects here. ... See also: Progress of the SARS outbreak and Severe acute respiratory syndrome. ... Binomial name Maupas, 1900 Caenorhabditis elegans (IPA: ) is a free-living nematode (roundworm), about 1 mm in length, which lives in temperate soil environments. ... Classes Adenophorea    Subclass Enoplia    Subclass Chromadoria Secernentea    Subclass Rhabditia    Subclass Spiruria    Subclass Diplogasteria    Subclass Tylenchia The nematodes or roundworms (Phylum Nematoda from Greek (nema): thread + -ode like) are one of the most common phyla of animals, with over 20,000 different described species (over 15,000 are parasitic). ... Binomial name Danio rerio (Hamilton-Buchanan, 1822) The Zebra Danio or Zebrafish (Brachydanio rerio or Danio rerio) is a tropical fish, commonly kept in aquaria and used for scientific research, belonging to the minnow family (Cyprinidae). ... Binomial name Xenopus laevis Daudin, 1802 The African clawed frog (Xenopus laevis, also known as platanna) is a species of South African aquatic frog of the genus Xenopus. ... Binomial name Oryzias latipes Temminck & Schlegel 1846 The very small ricefish Oryzias latipes, also known as the medaka or Japanese killifish, is a popular aquarium fish native to Southeast Asia. ... For other uses, see Fugu (disambiguation). ... For other uses, see Tomato (disambiguation). ... Binomial name Apis mellifera The species called Western honeybees (Apis mellifera) are honeybees comprised of several subspecies or races. ... It has been suggested that Veraison be merged into this article or section. ... Binomial name Vitis vinifera L. For thousands of years, the fruit and plant of Vitis vinifera, the European grapevine, have been harvested for both medicinal and nutritional value; its history is intimately entwined with the history of wine. ... The 1918 flu pandemic, commonly referred to as the Spanish flu, was a category 5 influenza pandemic caused by an unusually severe and deadly Influenza A virus strain of subtype H1N1. ...

See also

The Honey Bee Genome Sequencing Consortium is an international collaborative group of genomics scientists, scientific organisations and universities who are trying to decipher the genome sequences of the honey bee (Apis mellifera). ... The goal of the International HapMap Project is to develop a haplotype map of the human genome, also referred to as the HapMap, which will describe the common patterns of human genetic variation. ... National Center for Biotechnology Information logo The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. ... The Joint Genome Institute Production Genomics Facility is located in Walnut Creek, California. ... A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. ... This list of sequenced archaeal genomes contains all the archaeal known to have publically available complete genome sequences that have been assembled, annotated and published; draft genomes are not included. ... The nematode worm Caenorhabditis elegans was the first multicellular organism to have its complete genome sequence determined. ... The IGGPs main goals are to improve control, yield and quality in wine grape production via genetic modification The International Grape Genomics Program (IGGP) is a collaborative genome project dedicated to determining the genome sequence of the grapevine, Vitis vinifera L. As the name suggests, it is a multi...

External links

  • GOLD:Genomes OnLine Database
  • Genome Project Database
  • BFAB functional annotation resources to benchmark and to develop new annotation methods
  • SEED The SEED database, an open source database for genome annotation.
  • IMG The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI.
  • IMG/M The Integrated Microbial Genomes system, for metagenome analysis by the DOE-JGI.
  • PUMA2 Integrated Grid based system for the comparative analysis of genomes and metabolic reconstructions.
Genomics topics
Genome project | Paleopolyploidy | Glycomics | Human Genome Project | Proteomics
Chemogenomics | Structural genomics | Pharmacogenetics | Pharmacogenomics | Toxicogenomics | Computational genomics
Bioinformatics | Cheminformatics | Systems biology

  Results from FactBites:
 
Genome - Wikipedia, the free encyclopedia (975 words)
The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.
Since genomes and their organisms are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive.
Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products.
  More results at FactBites »

 
 

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