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CDinFusion - Submission-Ready, On-Line Integration of Sequence and Contextual Data

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Hankeln,  W.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Wendel,  N. J.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Gerken,  J.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Waldmann,  J.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Buttigieg,  P. L.
HGF MPG Joint Research Group for Deep Sea Ecology & Technology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Kostadinov,  I.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Kottmann,  R.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Yilmaz,  P.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Glöckner,  F. O.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Hankeln11.PDF
(Publisher version), 348KB

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Citation

Hankeln, W., Wendel, N. J., Gerken, J., Waldmann, J., Buttigieg, P. L., Kostadinov, I., et al. (2011). CDinFusion - Submission-Ready, On-Line Integration of Sequence and Contextual Data. PLoS One, 6(9): e24797.


Cite as: http://hdl.handle.net/21.11116/0000-0001-C917-3
Abstract
State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental data, as well as information about the environment are rarely submitted along with the sequence data. If these contextual or metadata are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence data collection and to promote the capturing, exchange and integration of sequence data with contextual data. In a recent community effort the GSC has developed a series of recommendations for contextual data that should be submitted along with sequence data. To support the scientific community to significantly enhance the quality and quantity of contextual data in the public sequence data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate contextual and sequence data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.