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

• 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.

Ämnesord

NATURVETENSKAP  -- Biologiska vetenskaper -- Mikrobiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Microbiology (hsv//eng)

NATURVETENSKAP  -- Biologiska vetenskaper -- Zoologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Zoology (hsv//eng)

NATURVETENSKAP  -- Biologiska vetenskaper -- Bioinformatik och systembiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)

NATURVETENSKAP  -- Biologiska vetenskaper -- Ekologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Ecology (hsv//eng)

NATURVETENSKAP  -- Biologiska vetenskaper -- Biologisk systematik (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Biological Systematics (hsv//eng)

LANTBRUKSVETENSKAPER  -- Lantbruksvetenskap, skogsbruk och fiske -- Markvetenskap (hsv//swe)

AGRICULTURAL SCIENCES  -- Agricultural Science, Forestry and Fisheries -- Soil Science (hsv//eng)

Nyckelord

Mikrobiologi

Microbiology

Morfologi

Morphology

Systematik och fylogeni

Systematics and phylogenetics

Terrestisk ekologi

Terrestrial ecology

Bioinformatik

Bioinformatics

Jordmånslära

Pedology

Markbiologi

Soil biology

Bioinformatik

Bioinformatics

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

Publikations- och innehållstyp

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