Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Oct 22:8:406.
doi: 10.1186/1471-2105-8-406.

MetaLook: a 3D visualisation software for marine ecological genomics

Thierry Lombardot  1 , Renzo Kottmann, Gregory Giuliani, Andrea de Bono, Nans Addor, Frank Oliver Glöckner
Affiliations

MetaLook: a 3D visualisation software for marine ecological genomics

Thierry Lombardot et al. BMC Bioinformatics. .

Abstract

Background: Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenomes of environmental relevance must take into account the corresponding habitat (contextual) data, e.g. water depth, physical and chemical parameters. The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis.

Results: We implemented the MetaLook software for visualisation and analysis of marine ecological genomic and metagenomic data with respect to habitat parameters. MetaLook offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a centralised georeferenced database. The user can define environmental containers to organise the sequences according to different habitat criteria. To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported sequences, using the BLAST algorithm. This allows an interactive assessment of the distribution of gene functions in the environment.

Conclusion: MetaLook allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. This software is a step towards the creation of specialised tools to study constrained distributions and habitat specificity of genes correlated with specific processes. MetaLook is available at: http://www.megx.net/metalook.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Client/Server architecture of MetaLook. The Java3D client runs on a local machine and gets data from the PostgreSQL server through HTTP request in XML format. DNA sequences of interest can be up- and downloaded for further analysis.
Figure 2
Figure 2
The environmental containers in MetaLook. DNA sequences of genomes and metagenomes can be sorted into 3D containers according to habitat information such as e.g. water column vs. sediments, depth profile or physical-chemical parameters. The geographic origins of the DNA sequence samples in each container are shown on the world map.
Figure 3
Figure 3
Displaying (meta)-genomes and genes in MetaLook. Each container can be opened to display the DNA sequence and the genes of each genome and metagenomic fragment. Genes can further be selected for download or analysis.
Figure 4
Figure 4
Study of the habitat-specificity of a gene. Here, the gene encoding a photolyase (foreground) shows BLASTP hits in the top layers of the ocean, as expected, but also some unexpected hits in the deep sea (container 7).
Figure 5
Figure 5
Study of the habitat-specificity of a gene (habitat parameters). a) Information for an unexpected BLASTP hit of the photolyase gene from figure 4 with a sequence originating from a deep-sea sample; b) BLASTP sequence alignment for the corresponding sequences.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Field D, Kyrpides N. The Positive Role of the Ecological Community in the Genomic Revolution. Microb Ecol. 2007;53:507–511. doi: 10.1007/s00248-007-9206-5. - DOI - PubMed
    1. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 2007;5:e77. doi: 10.1371/journal.pbio.0050077. - DOI - PMC - PubMed
    1. International Nucleotide Sequence Database Collaboration http://www.insdc.org
    1. The Genomic Standards Consortium (GSC) http://darwin.nox.ac.uk/gsc/gcat
    1. Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D. Concept of sample in OMICS technology. OMICS. 2006;10:127–137. doi: 10.1089/omi.2006.10.127. - DOI - PubMed

Publication types