I. Alam, A. Antunes, A.A. Kamau, W. alawi Ba, M. Kalkatawi, U. Stingl, V.B. Bajic
PLoS One, 8(12):e82210, (2013)
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.
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.
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)