FANTOM: Functional and taxonomic analysis of metagenomes

BMC Bioinformatics

Jens Nielsen¹  Intawat Nookaew¹  Fredrik H Karlsson¹  Kemal Sanli² 

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

[2]Present Address: Department of Biological and Environmental Sciences, University of Gothenburg, Box 100, Gothenburg, S-405 30, Sweden

关键词: Visualization;    Multivariate analysis;    Statistical analysis;    Metagenomics;    Graphical User Interface (GUI);   

Others  :  1087996
DOI  :  10.1186/1471-2105-14-38

 received in 2012-09-27, accepted in 2013-01-29,  发布年份 2013

【 摘 要 】

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. webcite

【 授权许可】

   
2013 Sanli et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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