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PlutoF—a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences

Abarenkov, Kessy (author)
Tedersoo, L. (author)
Nilsson, R. Henrik, 1976 (author)
Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences
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Vellak, Kai (author)
Saar, Irja (author)
Veldre, Vilmar (author)
Parmasto, Erast (author)
Prous, Marko (author)
Aan, Anne (author)
Ots, Margus (author)
Kurina, Olavi (author)
Ostonen, Ivika (author)
Jõgeva, Janno (author)
Halapuu, Siim (author)
Põldmaa, Kadri (author)
Toots, Märt (author)
Truu, Jaak (author)
Larsson, Karl-Henrik, 1948 (author)
Kõljalg, Urmas (author)
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 (creator_code:org_t)
2010
2010
English.
In: Evolutionary Bioinformatics. - 1176-9343. ; 6, s. 189-196
Related links:
https://gup.ub.gu.se...
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https://doi.org/10.4...
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.

Subject headings

NATURVETENSKAP  -- Biologi -- Biologisk systematik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Biological Systematics (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  -- Biologi -- Zoologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Zoology (hsv//eng)
LANTBRUKSVETENSKAPER  -- Lantbruksvetenskap, skogsbruk och fiske -- Markvetenskap (hsv//swe)
AGRICULTURAL SCIENCES  -- Agriculture, Forestry and Fisheries -- Soil Science (hsv//eng)
NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)

Keyword

Sequence management environment ; data mining ; metadata ; thin clients ; sequence identification

Publication and Content Type

ref (subject category)
art (subject category)

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