MetaLook: a 3D visualisation software for marine ecological genomics

<p>Abstract</p> <p>Background</p> <p>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 relev...

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Main Authors: Addor Nans, de Bono Andrea, Giuliani Gregory, Kottmann Renzo, Lombardot Thierry, Glöckner Frank
Format: Article
Language:English
Published: BMC 2007-10-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/8/406
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spelling doaj-6513560d700f4148b7806609e55d61772020-11-24T23:07:51ZengBMCBMC Bioinformatics1471-21052007-10-018140610.1186/1471-2105-8-406MetaLook: a 3D visualisation software for marine ecological genomicsAddor Nansde Bono AndreaGiuliani GregoryKottmann RenzoLombardot ThierryGlöckner Frank<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>environmental containers </it>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.</p> <p>Conclusion</p> <p>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.</p> <p>MetaLook is available at: <url>http://www.megx.net/metalook</url></p> http://www.biomedcentral.com/1471-2105/8/406
collection DOAJ
language English
format Article
sources DOAJ
author Addor Nans
de Bono Andrea
Giuliani Gregory
Kottmann Renzo
Lombardot Thierry
Glöckner Frank
spellingShingle Addor Nans
de Bono Andrea
Giuliani Gregory
Kottmann Renzo
Lombardot Thierry
Glöckner Frank
MetaLook: a 3D visualisation software for marine ecological genomics
BMC Bioinformatics
author_facet Addor Nans
de Bono Andrea
Giuliani Gregory
Kottmann Renzo
Lombardot Thierry
Glöckner Frank
author_sort Addor Nans
title MetaLook: a 3D visualisation software for marine ecological genomics
title_short MetaLook: a 3D visualisation software for marine ecological genomics
title_full MetaLook: a 3D visualisation software for marine ecological genomics
title_fullStr MetaLook: a 3D visualisation software for marine ecological genomics
title_full_unstemmed MetaLook: a 3D visualisation software for marine ecological genomics
title_sort metalook: a 3d visualisation software for marine ecological genomics
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2007-10-01
description <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>environmental containers </it>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.</p> <p>Conclusion</p> <p>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.</p> <p>MetaLook is available at: <url>http://www.megx.net/metalook</url></p>
url http://www.biomedcentral.com/1471-2105/8/406
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