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analysis starts with collecting reads from any shotgun platform. Then, the reads are compared with sequence databases using BLAST or similar. Third, MEGAN assigns a taxon ID to processed read results based on NCBI taxonomy which creates a MEGAN file that contains required information for statistical
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is the study of genomic content of samples from same habitat, which is designed to determine the role and the extent of species diversity. Targeted or random sequencing are widely used with comparisons against sequence databases. Recent developments in sequencing technology increased the number of
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Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (April 2004). "Environmental Genome
Shotgun
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Poinar, Hendrik N.; Carsten
Schwarz; Ji Qi; Beth Shapiro; Ross D. E. MacPhee; Bernard Buigues; Alexei Tikhonov; Daniel Huson; Lynn P. Tomsho; Alexander Auch; Markus Rampp; Webb Miller; Stephan C. Schuster (2007).
268:) algorithm can be run to inspect assignments, to analyze data and to create summaries of data based on different NCBI taxonomy levels. LCA algorithm simply finds the lowest common ancestor of different species.
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techniques in particular, such as MEGAN, are designed to sample and investigate the unknown biodiversity of environmental samples where more precise techniques with smaller, better known samples, cannot be used.
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or another sequence comparison tool to assemble the segments into discrete comparable sequences. MEGAN is then used to compare the resulting sequences with gene sequences from
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and viral agents in the environment is far greater than previously estimated. Tools that allow the investigation of very large data sets from environmental samples using
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Frias-Lopez, Jorge; Yanmei Shi; Gene W. Tyson; Maureen L. Coleman; Stephan C. Schuster; Sallie W. Chisholm; band Edward F. DeLong (March 11, 2008).
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is an easy to use tool for analysing such metagenomics data. First version of MEGAN was released in 2007 and the most recent version is
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sample. A large term goal of most metagenomics is to inventory and measure the extent and the role of
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Fragments of DNA from an metagenomics sample, such as ocean waters or soil, are compared against
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Huson, Daniel H; S. Beier; I. Flade; A. Gorska; M. El-Hadidi; H. Ruscheweyh; R. Tappu (2016).
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Metagenomics is the analysis of the genomic sequences from a usually uncultured
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