deFUME specifications


Unique identifier OMICS_32534
Name deFUME
Interface Web user interface
Restrictions to use None
Input data Some nucleotide sequences generated from next generation sequencing technologies.
Input format FASTA,AB1
Output data The sequencing reads, the assembled contigs, predicted ORFs, BLASTp hits and InterPro functional data.
Output format FASTA,CSV
Programming languages Javascript, Perl, PHP
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes




  • person_outline Eric van der Helm

Additional information

Publication for deFUME

deFUME citations


Enterococcus faecalis AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells

Front Immunol
PMCID: 5915459
PMID: 29720977
DOI: 10.3389/fimmu.2018.00790

[…] sequenced at the Australian Genomic Research Facility (Brisbane, Australia) using primers 530F and 907R (). The individual sequence reads were trimmed to remove low quality bases and assembled using deFUME (). The assembled sequence was then aligned against the Ribosomal Database Project () core set of aligned rrs sequences and E. faecalis AHG0090 was identified using the Classifier and SeqMatch […]


deFUME: Dynamic exploration of functional metagenomic sequencing data

BMC Res Notes
PMCID: 4520277
PMID: 26227142
DOI: 10.1186/s13104-015-1281-y

[…] ily generated over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. To address this challenge we developed deFUME; an easy-to-use web server that automatically processes and annotates large amounts of sequencing data obtained through functional selections. […]

deFUME institution(s)
Supported by the European Union Seventh Framework Programme-ITN [FP7/2012/317058]; Novozymes A/S; the European Union Seventh Framework Programme (FP7-KBBE-2013-7-singlestage) under grant agreement no. 613745, Promys and the Novo Nordisk Foundation.

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