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Megraft: A software...
Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes
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- Bengtsson-Palme, Johan, 1985 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Department of Biological and Environmental Sciences,Institute of Neuroscience and Physiology, Department of Physiology,University of Gothenburg
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Hartmann, Martin (author)
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Unterseher, Martin (author)
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Vaishampayan, Parag (author)
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Abarenkov, Kessy (author)
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Durso, Lisa (author)
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Bik, Elisabeth M. (author)
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Garey, James R. (author)
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- Eriksson, Martin, 1970 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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(creator_code:org_t)
- Elsevier BV, 2012
- 2012
- English.
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508. ; 163:6-7, s. 407-412
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Abstract
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- Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package – Megraft – that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.
Subject headings
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Keyword
- Metagenomics
- Rarefaction
- Species richness analysis
- rDNA
- 16S
- 18S
- diversitetsanalys
- Species richness analysis
Publication and Content Type
- ref (subject category)
- art (subject category)
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Bengtsson-Palme, ...
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Hartmann, Martin
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Unterseher, Mart ...
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Vaishampayan, Pa ...
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Abarenkov, Kessy
-
Durso, Lisa
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show more...
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Bik, Elisabeth M ...
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Garey, James R.
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Eriksson, Martin ...
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Nilsson, R. Henr ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biological Syste ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Microbiology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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Research in Micr ...
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University of Gothenburg
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Chalmers University of Technology