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Improved software d...
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
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- Bengtsson-Palme, Johan, 1985 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Institute of Neuroscience and Physiology, Department of Physiology
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- Ryberg, Martin, 1976 (author)
- Uppsala universitet,Systematisk biologi
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- Hartmann, Martin (author)
- Eidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs,Forschungsanstalt Agroscope Reckenholz-Tanikon
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- Branco, Sara (author)
- University of California
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- Wang, Zheng, 1980 (author)
- Yale University
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- Godhe, Anna, 1967 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- De Wit, Pierre, 1978 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- Sánchez-García, Marisol (author)
- University of Tennessee
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- Ebersberger, Ingo (author)
- Johann Wolfgang Goethe Universität Frankfurt am Main,Goethe University Frankfurt
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- Sousa, Filipe de, 1982 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- Amend, Anthony S. (author)
- University of Hawaii
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- Jumpponen, Ari (author)
- Kansas State University
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- Unterseher, Martin (author)
- Universität Greifswald,University of Greifswald
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- Kristiansson, Erik, 1978 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics
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- Abarenkov, Kessy (author)
- Tartu Ülikool,University of Tartu
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- Bertrand, Yann (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- Sanli, Kemal, 1986 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- Eriksson, Martin, 1970 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Vik, Unni (author)
- Universitetet i Oslo,University of Oslo
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Veldre, Vilmar (author)
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- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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(creator_code:org_t)
- 2013
- 2013
- English.
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In: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
- Related links:
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https://gup.ub.gu.se... (primary) (free)
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https://research.cha...
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https://doi.org/10.1...
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https://gup.ub.gu.se...
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https://urn.kb.se/re...
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Abstract
Subject headings
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- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
Subject headings
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- LANTBRUKSVETENSKAPER -- Lantbruksvetenskap, skogsbruk och fiske -- Markvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agriculture, Forestry and Fisheries -- Soil Science (hsv//eng)
- LANTBRUKSVETENSKAPER -- Annan lantbruksvetenskap -- Miljö- och naturvårdsvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Other Agricultural Sciences -- Environmental Sciences related to Agriculture and Land-use (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- 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 -- 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 -- Data- och informationsvetenskap -- Datavetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Computer Sciences (hsv//eng)
Keyword
- molecular ecology
- next-generation sequencing
- Perl
- Fungi
- ribosomal DNA
- Fungi
- molecular ecology
- next-generation sequencing
- Perl
- ribosomal DNA
Publication and Content Type
- art (subject category)
- ref (subject category)
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Bengtsson-Palme, ...
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Ryberg, Martin, ...
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Hartmann, Martin
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Branco, Sara
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Wang, Zheng, 198 ...
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Godhe, Anna, 196 ...
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De Wit, Pierre, ...
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Sánchez-García, ...
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Ebersberger, Ing ...
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Sousa, Filipe de ...
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Amend, Anthony S ...
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Jumpponen, Ari
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Unterseher, Mart ...
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Kristiansson, Er ...
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Abarenkov, Kessy
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Bertrand, Yann
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Sanli, Kemal, 19 ...
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Eriksson, Martin ...
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Vik, Unni
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Veldre, Vilmar
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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 Botany
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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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- AGRICULTURAL SCIENCES
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AGRICULTURAL SCI ...
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and Agriculture Fore ...
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and Soil Science
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- AGRICULTURAL SCIENCES
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AGRICULTURAL SCI ...
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and Other Agricultur ...
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and Environmental Sc ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Ecology
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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 Computer and Inf ...
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and Bioinformatics
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Microbiology in ...
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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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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Zoology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Computer Science ...
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- Articles in the publication
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Methods in Ecolo ...
- By the university
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Chalmers University of Technology
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University of Gothenburg
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Uppsala University