Abstract
BackgroundFunctional 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.FindingsHere 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.ConclusionThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1281-y) contains supplementary material, which is available to authorized users.
Highlights
Functional metagenomic selections represent a powerful technique that is widely applied for iden‐ tification of novel genes from complex metagenomic sources
The translated Open reading frames (ORFs) are aligned to the nr protein database using BLASTp [12] and submitted to InterPro [13]
To demonstrate and test the deFUME web server, we analyzed Sanger sequencing data derived from a functional metagenomics selection for genes conferring tolerance of E. coli to high levels of lysine
Summary
Functional metagenomic selections represent a powerful technique that is widely applied for iden‐ tification of novel genes from complex metagenomic sources. DNA inserts from clones exhibiting the desired phenotype can be sequenced, enabling functional isolation of novel genes. *Correspondence: evand@biosustain.dtu.dk 1 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark Full list of author information is available at the end of the article Data analysis is performed including BLAST searches and other functional annotations.
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