Dataset Information

G-InforBIO: integrated system for microbial genomics.

ABSTRACT: BACKGROUND: Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs. RESULTS: The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses. CONCLUSION: The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site.

SUBMITTER: Tanaka N

PROVIDER: S-EPMC1552091 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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G-InforBIO: integrated system for microbial genomics.

Tanaka Naoto N Abe Takashi T Miyazaki Satoru S Sugawara Hideaki H

BMC bioinformatics 20060804

<h4>Background</h4>Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs.<h4>Results</h4>The G-InforBIO system is a novel tool for genome data management and sequ ...[more]

PMID: 16887044

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Project description:BackgroundBioelectrochemical systems have been considered a promising novel technology that shows an enhanced energy recovery, as well as generation of value-added products. A number of recent studies suggested that an enhancement of carbon conversion and biogas production can be achieved in an integrated system of microbial electrolysis cell (MEC) and anaerobic digestion (AD) for waste activated sludge (WAS). Microbial communities in integrated system would build a thorough energetic and metabolic interaction network regarding fermentation communities and electrode respiring communities. The characterization of integrated community structure and community shifts is not well understood, however, it starts to attract interest of scientists and engineers.ResultsIn the present work, energy recovery and WAS conversion are comprehensively affected by typical pretreated biosolid characteristics. We investigated the interaction of fermentation communities and electrode respiring communities in an integrated system of WAS fermentation and MEC for hydrogen recovery. A high energy recovery was achieved in the MECs feeding WAS fermentation liquid through alkaline pretreatment. Some anaerobes belonging to Firmicutes (Acetoanaerobium, Acetobacterium, and Fusibacter) showed synergistic relationship with exoelectrogens in the degradation of complex organic matter or recycling of MEC products (H2). High protein and polysaccharide but low fatty acid content led to the dominance of Proteiniclasticum and Parabacteroides, which showed a delayed contribution to the extracellular electron transport leading to a slow cascade utilization of WAS.ConclusionsEfficient pretreatment could supply more short-chain fatty acids and higher conductivities in the fermentative liquid, which facilitated mass transfer in anodic biofilm. The overall performance of WAS cascade utilization was substantially related to the microbial community structures, which in turn depended on the initial pretreatment to enhance WAS fermentation. It is worth noting that species in AD and MEC communities are able to build complex networks of interaction, which have not been sufficiently studied so far. It is therefore important to understand how choosing operational parameters can influence reactor performances. The current study highlights the interaction of fermentative bacteria and exoelectrogens in the integrated system.

Project description:BACKGROUND: We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile Haloarcula marismortui; (2) the non-pigmented Natrialba asiatica; (3) the psychrophile Halorubrum lacusprofundi and (4) the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe. RESULTS: As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI) for their predicted proteins. Multiple insertion sequence (IS) elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP) and transcription factor IIB (TFB) homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi. CONCLUSION: Despite the diverse habitats of these species, all five halophiles share (1) high GC content and (2) low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the IS-element rich genome of H. sp. NRC-1. Identification of multiple TBP and TFB homologs in these four halophiles are consistent with the hypothesis that different types of complex transcriptional regulation may occur through multiple TBP-TFB combinations in response to rapidly changing environmental conditions. Low-pass shotgun sequence analyses of genomes permit extensive and diverse analyses, and should be generally useful for comparative microbial genomics.

Dataset Information

G-InforBIO: integrated system for microbial genomics.

Publications

G-InforBIO: integrated system for microbial genomics.

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