deFUME: Dynamic exploration of functional metagenomic sequencing data

Eric van der Helm; Henrik Marcus Geertz-Hansen; Hans Jasper Genee; Sailesh Malla; Morten Otto Alexander Sommer

doi:10.1186/s13104-015-1281-y

deFUME: Dynamic exploration of functional metagenomic sequencing data

Eric van der Helm, Henrik Marcus Geertz-Hansen, Hans Jasper Genee, Sailesh Malla, Morten Otto Alexander Sommer

Novo Nordisk Foundation Center for Biosustainability

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Abstract

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

Original language	English
Journal	BMC Research Notes
Volume	8
Issue number	328
Pages (from-to)	328
Number of pages	1
ISSN	1756-0500
DOIs	https://doi.org/10.1186/s13104-015-1281-y
Publication status	Published - 2015

Bibliographical note

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons. org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Keywords

Functional metagenomics
Web services
Visualization
Sequence analysis
Gene ontology

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10.1186/s13104-015-1281-y

DeFUMEFinal published version, 0.98 MB

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BacTory: Biorefinery Training Platform: Bacterial Factories for Sustainable Chemical and Drug Production
Molin, S., Nørholm, M., Cavaleiro, M., Machado, H., Wendel, S., van der Helm, E., Bojanovic, K., Vazquez Albacete, D., D'Arrigo, I., Li, S., Yang, X., Redl, S. M. A., Pogrebnyakov, I., Lehning, C. E., Giubergia, S., Calero Valdayo, P. M. & Lohmann, R.
01/10/2012 → 31/01/2017
Project: Research

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abstract = "Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.",

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deFUME: Dynamic exploration of functional metagenomic sequencing data

Abstract

Bibliographical note

Keywords

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Projects

BacTory: Biorefinery Training Platform: Bacterial Factories for Sustainable Chemical and Drug Production

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