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

被引：226

作者：

Abarenkov, Kessy ^{[1
,2
]}

Tedersoo, Leho ^{[1
,2
]}

Nilsson, R. Henrik ^{[2
,3
]}

Vellak, Kai ^{[2
]}

Saar, Irja ^{[2
]}

Veldre, Vilmar ^{[2
]}

Parmasto, Erast ^{[1
,4
]}

Prous, Marko ^{[2
]}

Aan, Anne ^{[1
]}

Ots, Margus ^{[1
]}

Kurina, Olavi ^{[4
]}

Ostonen, Ivika ^{[2
]}

Jogeva, Janno ^{[1
]}

Halapuu, Siim ^{[1
]}

Poldmaa, Kadri ^{[2
]}

Toots, Maert ^{[2
,5
]}

Truu, Jaak ^{[6
]}

Larsson, Karl-Henrik ^{[7
]}

Koljalg, Urmas ^{[1
,2
]}

机构：

[1] Univ Tartu, Nat Hist Museum, EE-51014 Tartu, Estonia

[2] Univ Tartu, Inst Ecol & Earth Sci, EE-51014 Tartu, Estonia

[3] Univ Gothenburg, Dept Plant & Environm Sci, S-40530 Gothenburg, Sweden

[4] Estonian Univ Life Sci, Inst Agr & Environm, EE-51014 Tartu, Estonia

[5] Univ Tartu, Inst Stat, EE-50409 Tartu, Estonia

[6] Univ Tartu, Inst Mol & Cell Biol, EE-51010 Tartu, Estonia

[7] Univ Oslo, Nat Hist Museum, N-0318 Oslo, Norway

来源：

EVOLUTIONARY BIOINFORMATICS | 2010年 / 6卷

关键词：

sequence management environment; data mining; metadata; thin clients; sequence identification; MYCORRHIZAL FUNGI; MOLECULAR-IDENTIFICATION; DATABASE; GENERATION; PHYLOGENY; DIVERSITY; PATTERNS; GENBANK; REVEAL; UNITE;

D O I：

10.4137/EBO.S6271

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：189 / 196

页数：8

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