INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

<h4>Background</h4>The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from...

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Autores principales:	Intikhab Alam, André Antunes, Allan Anthony Kamau, Wail Ba Alawi, Manal Kalkatawi, Ulrich Stingl, Vladimir B Bajic
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9bc6a0e2ce31421fbfdba2925a56f87b
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spelling	oai:doaj.org-article:9bc6a0e2ce31421fbfdba2925a56f87b2021-11-18T08:43:07ZINDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.1932-620310.1371/journal.pone.0082210https://doaj.org/article/9bc6a0e2ce31421fbfdba2925a56f87b2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24324765/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.<h4>Results</h4>We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments.<h4>Conclusions</h4>We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.Intikhab AlamAndré AntunesAllan Anthony KamauWail Ba AlawiManal KalkatawiUlrich StinglVladimir B BajicPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 12, p e82210 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Intikhab Alam André Antunes Allan Anthony Kamau Wail Ba Alawi Manal Kalkatawi Ulrich Stingl Vladimir B Bajic INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.
description	<h4>Background</h4>The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.<h4>Results</h4>We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments.<h4>Conclusions</h4>We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.
format	article
author	Intikhab Alam André Antunes Allan Anthony Kamau Wail Ba Alawi Manal Kalkatawi Ulrich Stingl Vladimir B Bajic
author_facet	Intikhab Alam André Antunes Allan Anthony Kamau Wail Ba Alawi Manal Kalkatawi Ulrich Stingl Vladimir B Bajic
author_sort	Intikhab Alam
title	INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.
title_short	INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.
title_full	INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.
title_fullStr	INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.
title_full_unstemmed	INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.
title_sort	indigo - integrated data warehouse of microbial genomes with examples from the red sea extremophiles.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/9bc6a0e2ce31421fbfdba2925a56f87b
work_keys_str_mv	AT intikhabalam indigointegrateddatawarehouseofmicrobialgenomeswithexamplesfromtheredseaextremophiles AT andreantunes indigointegrateddatawarehouseofmicrobialgenomeswithexamplesfromtheredseaextremophiles AT allananthonykamau indigointegrateddatawarehouseofmicrobialgenomeswithexamplesfromtheredseaextremophiles AT wailbaalawi indigointegrateddatawarehouseofmicrobialgenomeswithexamplesfromtheredseaextremophiles AT manalkalkatawi indigointegrateddatawarehouseofmicrobialgenomeswithexamplesfromtheredseaextremophiles AT ulrichstingl indigointegrateddatawarehouseofmicrobialgenomeswithexamplesfromtheredseaextremophiles AT vladimirbbajic indigointegrateddatawarehouseofmicrobialgenomeswithexamplesfromtheredseaextremophiles
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INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

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