Search: hsv:(NATURVETENSKAP) hsv:(Biologi) hsv:(Bioinformatik och systembiologi) >
Metaxa2 Database Bu...
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
-
- Bengtsson-Palme, Johan, 1985 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,CARe - Centrum för antibiotikaresistensforskning,Institute of Biomedicine, Department of Infectious Medicine,Centre for antibiotic resistance research, CARe,University of Wisconsin Madison,University of Gothenburg
-
Richardson, Rodney T (author)
-
- Meola, Marco (author)
- Forschungsanstalt Agroscope Changins-Wadenswil
-
show more...
-
- Wurzbacher, Christian, 1980 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg,Technische Universität München (TUM),Technical University of Munich (TUM)
-
- Tremblay, Émilie D (author)
- Canadian Food Inspection Agency (CFIA)
-
- Thorell, Kaisa, 1983 (author)
- Karolinska Institutet
-
- Kanger, Kärt (author)
- Tartu Ülikool,University of Tartu
-
- Bilodeau, Guillaume J (author)
- Canadian Food Inspection Agency (CFIA)
-
Johnson, Reed M (author)
-
- Hartmann, Martin (author)
- Eidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs,Eidgenössische Technische Hochschule Zürich (ETH),Swiss Federal Institute of Technology in Zürich (ETH)
-
- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
-
- Eriksson, Martin, 1970 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
-
show less...
-
(creator_code:org_t)
- 2018-06-15
- 2018
- English.
-
In: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 34:23, s. 4027-4033
- Related links:
-
https://academic.oup...
-
show more...
-
https://research.cha... (primary) (free)
-
https://gup.ub.gu.se...
-
https://doi.org/10.1...
-
https://research.cha...
-
http://kipublication...
-
show less...
Abstract
Subject headings
Close
- Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.
Subject headings
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Zoologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Zoology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- Metabarcoding ; 16S ; 18S ; ITS ; database builder ; sof
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
-
Bengtsson-Palme, ...
-
Richardson, Rodn ...
-
Meola, Marco
-
Wurzbacher, Chri ...
-
Tremblay, Émilie ...
-
Thorell, Kaisa, ...
-
show more...
-
Kanger, Kärt
-
Bilodeau, Guilla ...
-
Johnson, Reed M
-
Hartmann, Martin
-
Nilsson, R. Henr ...
-
Eriksson, Martin ...
-
show less...
- About the subject
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Microbiology
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Computer and Inf ...
-
and Bioinformatics
-
- MEDICAL AND HEALTH SCIENCES
-
MEDICAL AND HEAL ...
-
and Basic Medicine
-
and Microbiology in ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Biological Syste ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Botany
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Ecology
-
show more...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Bioinformatics a ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Zoology
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Genetics
-
show less...
- Articles in the publication
-
Bioinformatics ( ...
- By the university
-
University of Gothenburg
-
Chalmers University of Technology
-
Karolinska Institutet