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Spades
SPAdes (St. Petersburg genome assembler) is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. Therefore, it might not be suitable for large genomes projects. SPAdes works with Ion Torrent, PacBio, Oxford Nanopore, and Illumina paired-end, mate-pairs and single reads. SPAdes has been integrated into Galaxy pipelines by Guy Lionel and Philip Mabon. Background Studying the genome of single cells will help to track changes that occur in DNA over time or associated with exposure to different conditions. Additionally, many projects such as Human Microbiome Project and antibiotics discovery would greatly benefit from Single-cell sequencing (SCS). SCS has an advantage over sequencing DNA extracted from large number of cells. The problem of averaging out the significant variations between cells can be overcome by using SCS. Experimental and computational technologies are being optimized to allow researchers to sequence single cel ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Assembler (bioinformatics)
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. Typically, the short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript ( ESTs). The problem of sequence assembly can be compared to taking many copies of a book, passing each of them through a shredder with a different cutter, and piecing the text of the book back together just by looking at the shredded pieces. Besides the obvious difficulty of this task, there are some extra practical issues: the original may have many repeated paragraphs, and some shreds may be modified during shredding to have typos. Excerpts from another book may also be added in, and some shreds may be completely unrecognizable. Genome ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Velvet Assembler
Velvet is an algorithm package that has been designed to deal with ''de novo'' genome assembly and short read sequencing alignments. This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the removal of errors and the simplification of repeated regions.Zerbino, D. R.; Birney, E. (2008)"Velvet: de novo assembly using very short reads" Retrieved 18 October 2013. Velvet has also been implemented in commercial packages, such as Sequencher, Geneious, MacVector and BioNumerics. Introduction The development of next-generation sequencers (NGS) allowed for increased cost effectiveness on very short read sequencing. The manipulation of de Bruijn graphs as a method for alignment became more realistic but further developments were needed to address issues with errors and repeats. This led to the development of Velvet by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute in the United Kingdom. Velvet works by efficiently manipul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Saint Petersburg State University
Saint Petersburg State University (SPBU; russian: Санкт-Петербургский государственный университет) is a public research university in Saint Petersburg, Russia. Founded in 1724 by a decree of Peter the Great, the university from the beginning has had a focus on fundamental research in science, engineering and humanities. During the Soviet period, it was known as Leningrad State University (russian: Ленинградский государственный университет). It was renamed after Andrei Zhdanov in 1948 and was officially called "Leningrad State University, named after A. A. Zhdanov and decorated with the Order of Lenin and the Order of the Red Banner of Labour." Zhdanov's was removed in 1989 and Leningrad in the name was officially replaced with Saint Petersburg in 1992. It is made up of 24 specialized faculties (departments) and institutes, the Academic Gymnasium, the Medical College, the College of Physical Culture ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequencing
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) 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 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 cover ... [...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] |
Edge (graph Theory)
This is a glossary of graph theory. Graph theory is the study of graphs, systems of nodes or vertices connected in pairs by lines or edges. Symbols A B C D E F G H I K L M N O ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vertice
In discrete mathematics, and more specifically in graph theory, a vertex (plural vertices) or node is the fundamental unit of which graphs are formed: an Graph (discrete mathematics)#Graph, undirected graph consists of a set of vertices and a set of Edge (graph theory), edges (unordered pairs of vertices), while a directed graph consists of a set of vertices and a set of arcs (ordered pairs of vertices). In a diagram of a graph, a vertex is usually represented by a circle with a label, and an edge is represented by a line or arrow extending from one vertex to another. From the point of view of graph theory, vertices are treated as featureless and indivisible Mathematical object, objects, although they may have additional structure depending on the application from which the graph arises; for instance, a semantic network is a graph in which the vertices represent concepts or classes of objects. The two vertices forming an edge are said to be the endpoints of this edge, and the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coverage2
Coverage may refer to: Filmmaking * Coverage (lens), the size of the image a lens can produce * Camera coverage, the amount of footage shot and different camera setups used in filming a scene * Script coverage, a short summary of a script, written by script readers to recommend whether a film should be made Media and journalism * Broadcasting, radio, television, etc. * News ("press coverage", "media coverage"), the communication of selected information on current events Music * Coverage, a Descendents/ALL cover band from Calgary, Alberta, Canada * ''Coverage'' (album), a 2003 album by Mandy Moore Science and technology * Code coverage measure used in software testing * Coverage (telecommunication), a measure of cell phone or radio connectivity * Coverage (information systems), a measure for the quality/completeness of an information service * Coverage (shot peening), a criterium for quality of shot peening introduced by J.O. Almen in the 1940s * Coverage data, the mapping o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coverage Single Cell Sequencing
Coverage may refer to: Filmmaking * Coverage (lens), the size of the image a lens can produce * Camera coverage, the amount of footage shot and different camera setups used in filming a scene * Script coverage, a short summary of a script, written by script readers to recommend whether a film should be made Media and journalism * Broadcasting, radio, television, etc. * News ("press coverage", "media coverage"), the communication of selected information on current events Music * Coverage, a Descendents/ALL cover band from Calgary, Alberta, Canada * ''Coverage'' (album), a 2003 album by Mandy Moore Science and technology * Code coverage measure used in software testing * Coverage (telecommunication), a measure of cell phone or radio connectivity * Coverage (information systems), a measure for the quality/completeness of an information service * Coverage (shot peening), a criterium for quality of shot peening introduced by J.O. Almen in the 1940s * Coverage data, the mapping o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
De Bruijn Graph
In graph theory, an -dimensional De Bruijn graph of symbols is a directed graph representing overlaps between sequences of symbols. It has vertices, consisting of all possible sequences of the given symbols; the same symbol may appear multiple times in a sequence. For a set of symbols the set of vertices is: :V=S^n=\. If one of the vertices can be expressed as another vertex by shifting all its symbols by one place to the left and adding a new symbol at the end of this vertex, then the latter has a directed edge to the former vertex. Thus the set of arcs (that is, directed edges) is :E=\. Although De Bruijn graphs are named after Nicolaas Govert de Bruijn, they were discovered independently by both De Bruijn and I. J. Good. Much earlier, Camille Flye Sainte-Marie implicitly used their properties. Properties * If , then the condition for any two vertices forming an edge holds vacuously, and hence all the vertices are connected, forming a total of edges. * Each vertex has ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
K-mer
In bioinformatics, ''k''-mers are substrings of length k contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which ''k''-mers are composed of nucleotides (''i.e''. A, T, G, and C), ''k''-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines. Usually, the term ''k''-mer refers to all of a sequence's subsequences of length k, such that the sequence AGAT would have four monomers (A, G, A, and T), three 2-mers (AG, GA, AT), two 3-mers (AGA and GAT) and one 4-mer (AGAT). More generally, a sequence of length L will have L - k + 1 ''k''-mers and n^ total possible ''k''-mers, where n is number of possible monomers (e.g. four in the case of DNA). Introduction ''k''-mers are simply length k subsequences. For example, all the possible ''k''-mers of a DNA sequence are shown below: A method of visualizi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chimera (genetics)
A genetic chimerism or chimera ( ) is a single organism composed of cells with more than one distinct genotype. In animals, this means an individual derived from two or more zygotes, which can include possessing blood cells of different blood types, subtle variations in form (phenotype) and, if the zygotes were of differing sexes, then even the possession of both female and male sex organs. Animal chimeras are produced by the merger of two (or more) embryos. In plant chimeras, however, the distinct types of tissue may originate from the same zygote, and the difference is often due to mutation during ordinary cell division. Normally, genetic chimerism is not visible on casual inspection; however, it has been detected in the course of proving parentage. Another way that chimerism can occur in animals is by organ transplantation, giving one individual tissues that developed from a different genome. For example, transplantation of bone marrow often determines the recipient's en ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
