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Hybrid Genome Assembly
In bioinformatics, hybrid genome assembly refers to utilizing various sequencing technologies to achieve the task of assembling a genome from fragmented, sequenced DNA resulting from shotgun sequencing. Genome assembly presents one of the most challenging tasks in genome sequencing as most modern DNA sequencing technologies can only produce reads that are, on average, 25-300 base pairs in length.Pop, M. (2009). Genome assembly reborn: recent computational challenges. Brief Bioinform, 10(4), 354-366. . This is orders of magnitude smaller than the average size of a genome (the genome of the octoploid plant ''Paris japonica'' is 149 billion base pairsPellicer, Jaume, Fay, Michael F., & Leitch, Ilia J. (2010). The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society, 164(1), 10-15. ). This assembly is computationally difficult and has some inherent challenges, one of these challenges being that genomes often contain complex tandem repeats of sequences that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
De Novo Transcriptome Assembly
''De novo'' transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome. Introduction As a result of the development of novel sequencing technologies, the years between 2008 and 2012 saw a large drop in the cost of sequencing. Per megabase and genome, the cost dropped to 1/100,000th and 1/10,000th of the price, respectively. Prior to this, only transcriptomes of organisms that were of broad interest and utility to scientific research were sequenced; however, these developed in 2010s high-throughput sequencing (also called next-generation sequencing) technologies are both cost- and labor- effective, and the range of organisms studied via these methods is expanding. Transcriptomes have subsequently been created for chickpea, planarians, '' Parhyale hawaiensis'', as well as the brains of the Nile crocodile, the corn snake, the bearded dragon, and the red-eared slider, to name just a few. Examining non-model organ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
2010–13 Haiti Cholera Outbreak
The 2010s Haiti cholera outbreak is the first modern large-scale outbreak of cholera—a disease once considered beaten back largely due to the invention of modern sanitation. The disease was reintroduced to Haiti in October 2010, not long after the disastrous earthquake earlier that year, and since then cholera has spread across the country and become endemic, causing high levels of both morbidity and mortality. Nearly 800,000 Haitians have been infected by cholera, and more than 9,000 have died, according to the United Nations (UN). Cholera transmission in Haiti today is largely a function of eradication efforts including WASH (water, sanitation, and hygiene), education, oral vaccination, and climate variability. Early efforts were made to cover up the source of the epidemic, but thanks largely to the investigations of journalist Jonathan M. Katz and epidemiologist Renaud Piarroux, it is widely believed to be the result of contamination by infected United Nations peacekeepers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Escherichia Coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escherichia'' that is commonly found in the lower intestine of warm-blooded organisms. Most ''E. coli'' strains are harmless, but some serotypes ( EPEC, ETEC etc.) can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls. Most strains do not cause disease in humans and are part of the normal microbiota of the gut; such strains are harmless or even beneficial to humans (although these strains tend to be less studied than the pathogenic ones). For example, some strains of ''E. coli'' benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by pathogenic bacteria. These mutually beneficial relationships between ''E. col ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
N50 Statistic
In computational biology, N50 and L50 are statistics of a set of contig or scaffold lengths. The ''N50'' is similar to a mean or median of lengths, but has greater weight given to the longer contigs. It is used widely in genome assembly, especially in reference to contig lengths within a draft assembly. There are also the related U50, UL50, UG50, UG50%, N90, NG50, and D50 statistics. To provide a better assessment of assembly output for viral and microbial datasets, a new metric called U50 should be used. The ''U50'' identifies unique, target-specific contigs by using a reference genome as baseline, aiming at circumventing some limitations that are inherent to the ''N50'' metric. The use of the ''U50'' metric allows for a more accurate measure of assembly performance by analyzing only the unique, non-overlapping contigs. Most viral and microbial sequencing have high background noise (i.e., host and other non-targets), which contributes to having a skewed, misrepresented ''N50'' v ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Celera Corporation
Celera is a subsidiary of Quest Diagnostics which focuses on genetic sequencing and related technologies. It was founded in 1998 as a business unit of Applera, spun off into an independent company in 2008, and finally acquired by Quest Diagnostics in 2011. History Originally headquartered in Rockville, Maryland (relocated to Alameda, California), it was established in May 1998 by PE Corporation (later renamed to Applera), with Dr. J. Craig Venter from The Institute for Genomic Research (TIGR) as its first president. While at TIGR, Venter and Hamilton Smith led the first successful effort to sequence an entire organism's genome, that of the ''Haemophilus influenzae'' bacterium. Celera was formed for the purpose of generating and commercializing genomic information. Its stock is a tracking stock of Applera, along with the tracking stock of Applera's larger Applied Biosystems Group business unit. Celera sequenced the human genome at a fraction of the cost of the publicly-funded H ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vibrio Cholerae
''Vibrio cholerae'' is a species of Gram-negative, facultative anaerobe and comma-shaped bacteria. The bacteria naturally live in brackish or saltwater where they attach themselves easily to the chitin-containing shells of crabs, shrimps, and other shellfish. Some strains of ''V. cholerae'' are pathogenic to humans and cause a deadly disease cholera, which can be derived from the consumption of undercooked or raw marine life species. ''V. cholerae'' was first described by Félix-Archimède Pouchet in 1849 as some kind of protozoa. Filippo Pacini correctly identified it as a bacterium and from him, the scientific name is adopted. The bacterium as the cause of cholera was discovered by Robert Koch in 1884. Sambhu Nath De isolated the cholera toxin and demonstrated the toxin as the cause of cholera in 1959. The bacterium has a flagellum at one pole and several pili throughout its cell surface. It undergoes respiratory and fermentative metabolism. Two serogroups called O1 and O139 ... [...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 currently under active development. Third generation sequencing technologies have the capability to produce substantially longer reads than second generation sequencing, also known as next-generation sequencing. Such an advantage has critical implications for both genome science and the study of biology in general. 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 be improvements to the high error rates. For applications that are more tolerant to error rates, such as structural variant calling, third generation sequencing has been found to outperform existing methods, even at a low depth of sequencing coverage. Current technologies Sequencing technologies with a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Third Generation Sequencing
Third or 3rd may refer to: Numbers * 3rd, the ordinal form of the cardinal number 3 * , a fraction of one third * 1⁄60 of a ''second'', or 1⁄3600 of a ''minute'' Places * 3rd Street (other) * Third Avenue (other) * Highway 3 Music Music theory *Interval number of three in a musical interval ** major third, a third spanning four semitones ** minor third, a third encompassing three half steps, or semitones **neutral third, wider than a minor third but narrower than a major third **augmented third, an interval of five semitones ** diminished third, produced by narrowing a minor third by a chromatic semitone *Third (chord), chord member a third above the root * Degree (music), three away from tonic **mediant, third degree of the diatonic scale ** submediant, sixth degree of the diatonic scale – three steps below the tonic **chromatic mediant, chromatic relationship by thirds *Ladder of thirds, similar to the circle of fifths Albums *'' Third/Sister Lovers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Workflow And Pipeline Of Hybrid Genome Assembly
A workflow consists of an orchestrated and repeatable pattern of activity, enabled by the systematic organization of resources into processes that transform materials, provide services, or process information. It can be depicted as a sequence of operations, the work of a person or group, the work of an organization of staff, or one or more simple or complex mechanisms. From a more abstract or higher-level perspective, workflow may be considered a view or representation of real work. The flow being described may refer to a document, service, or product that is being transferred from one step to another. Workflows may be viewed as one fundamental building block to be combined with other parts of an organization's structure such as information technology, teams, projects and hierarchies. Historical development The development of the concept of a workflow occurred above a series of loosely defined, overlapping eras. Beginnings in manufacturing The modern history of workflows ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bottleneck (software)
In software engineering, a bottleneck occurs when the capacity of an application or a computer system is limited by a single component, like the neck of a bottle slowing down the overall water flow. The bottleneck has the lowest throughput of all parts of the transaction path. As such, system designers will try to avoid bottlenecks and direct effort towards locating and tuning existing bottlenecks. Some examples of possible engineering bottlenecks are: a processor, a communication link, disk IO, etc. Any system or application will hit a bottleneck if the work arrives at a sufficiently fast pace. According to the theory of constraints when looking to improve the speed of processing, the point of the bottleneck, or hot spot's occurrence is the place to work on. A thought-provoking stipulation of the theory is that raising the efficiency of a process stage other than the constraint can generate even more delay. Tracking down bottlenecks (sometimes known as "hot spots" - sections o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hamiltonian Path
In the mathematical field of graph theory, a Hamiltonian path (or traceable path) is a path in an undirected or directed graph that visits each vertex exactly once. A Hamiltonian cycle (or Hamiltonian circuit) is a cycle that visits each vertex exactly once. A Hamiltonian path that starts and ends at adjacent vertices can be completed by adding one more edge to form a Hamiltonian cycle, and removing any edge from a Hamiltonian cycle produces a Hamiltonian path. Determining whether such paths and cycles exist in graphs (the Hamiltonian path problem and Hamiltonian cycle problem) are NP-complete. Hamiltonian paths and cycles are named after William Rowan Hamilton who invented the icosian game, now also known as ''Hamilton's puzzle'', which involves finding a Hamiltonian cycle in the edge graph of the dodecahedron. Hamilton solved this problem using the icosian calculus, an algebraic structure based on roots of unity with many similarities to the quaternions (also invented by Hami ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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