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BMC Bioinformatics. 2013 Feb 1;14:38. doi: 10.1186/1471-2105-14-38.

FANTOM: Functional and taxonomic analysis of metagenomes.

Author information

  • 1Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE 412 96, Sweden.

Abstract

BACKGROUND:

Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context.

RESULTS:

Here we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases.

CONCLUSIONS:

The software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom.

PMID:
23375020
PMCID:
PMC3566963
DOI:
10.1186/1471-2105-14-38
[PubMed - indexed for MEDLINE]
Free PMC Article
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