PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences-Reference-Cited by-同舟云学术

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

Published:2010-01 Issue: Volume:6 Page:EBO.S6271
ISSN:1176-9343
Container-title:Evolutionary Bioinformatics
language:en
Short-container-title:Evol Bioinform Online

Author:

Abarenkov Kessy¹²,Tedersoo Leho¹²,Nilsson R. Henrik²³,Vellak Kai²,Saar Irja²,Veldre Vilmar²,Parmasto Erast¹⁴,Prous Marko²,Aan Anne¹,Ots Margus¹,Kurina Olavi⁴,Ostonen Ivika²,Jõgeva Janno¹,Halapuu Siim¹,Põldmaa Kadri²,Toots Märt²⁵,Truu Jaak⁶,Larsson Karl-Henrik⁷,Kõljalg Urmas¹²

Affiliation:

1. Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia.

2. Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.

3. Department of Plant and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden.

4. Institute of Agriculture and Environment, Estonian University of Life Sciences, 181 Riia St., 51014 Tartu, Estonia.

5. Institute of Statistics, University of Tartu, 2 Liivi St., 50409 Tartu, Estonia.

6. Institute of Molecular and Cell Biology, University of Tartu, 23 Riia St., 51010 Tartu, Estonia.

7. Natural History Museum of Oslo University, Box 1172, Blindern, N-0318 Oslo, Norway.

Abstract

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 .

Publisher

SAGE Publications

Subject

Computer Science Applications,Genetics,Ecology, Evolution, Behavior and Systematics

Link

http://journals.sagepub.com/doi/pdf/10.4137/EBO.S6271

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