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Title: Databases for Microbiologists

Abstract

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. Finally, the purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.

Authors:
ORCiD logo [1]
+ Show Author Affiliations
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division; Univ. of Tennessee, Knoxville, TN (United States). Department of Microbiology
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); National Institues of Health
Sponsoring Org.:
USDOE
OSTI Identifier:
1327628
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Bacteriology
Additional Journal Information:
Journal Volume: 197; Journal Issue: 15; Journal ID: ISSN 0021-9193
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zhulin, Igor B. Databases for Microbiologists. United States: N. p., 2015. Web. doi:10.1128/JB.00330-15.
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Zhulin, Igor B. Databases for Microbiologists. United States. https://doi.org/10.1128/JB.00330-15
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Zhulin, Igor B. Tue . "Databases for Microbiologists". United States. https://doi.org/10.1128/JB.00330-15. https://www.osti.gov/servlets/purl/1327628.
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@article{osti_1327628,
title = {Databases for Microbiologists},
author = {Zhulin, Igor B.},
abstractNote = {Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. Finally, the purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.},
doi = {10.1128/JB.00330-15},
journal = {Journal of Bacteriology},
number = 15,
volume = 197,
place = {United States},
year = {Tue May 26 00:00:00 EDT 2015},
month = {Tue May 26 00:00:00 EDT 2015}
}
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https://doi.org/10.1128/JB.00330-15
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ECMDB: The E. coli Metabolome Database
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RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
journal, January 2013

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Bacteriome.org an integrated protein interaction database for E. coli
journal, December 2007

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xBASE2: a comprehensive resource for comparative bacterial genomics
journal, December 2007

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CDD: NCBI's conserved domain database
journal, November 2014

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OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
journal, November 2014

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ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes: ABCdb: transporter repertoires
journal, March 2006

Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014

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HelicoBase: a Helicobacter genomic resource and analysis platform
journal, January 2014

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
journal, October 2010

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The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
journal, January 2009

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The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
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Genome annotation: from sequence to biology
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EcoProDB: the Escherichia coli protein database
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PATRIC, the bacterial bioinformatics database and analysis resource
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BacMet: antibacterial biocide and metal resistance genes database
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tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis
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AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species
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ProOpDB: Prokaryotic Operon DataBase
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ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
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BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species
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BacMap: an interactive picture atlas of annotated bacterial genomes
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EuPathDB: a portal to eukaryotic pathogen databases
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ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage
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The COG database: an updated version includes eukaryotes
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VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA
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CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes
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Saccharomyces Genome Database: the genomics resource of budding yeast
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FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus
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T3DB: an integrated database for bacterial type III secretion system
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CATH: comprehensive structural and functional annotations for genome sequences
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SMART: recent updates, new developments and status in 2015
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ViralZone: recent updates to the virus knowledge resource
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AtlasT4SS: A curated database for type IV secretion systems
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The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
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CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips
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Phagocytosis-like cell engulfment by a planctomycete bacterium
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Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum
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Environmental dissemination of pathogenic Listeria monocytogenes in flowing surface waters in Switzerland
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Database resources of the National Center for Biotechnology Information
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Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
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BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species
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GeneDB--an annotation database for pathogens.
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Database resources of the National Center for Biotechnology Information
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BacMap: An interactive picture atlas of annotated bacterial genomes
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STRING v9.1: protein-protein interaction networks, with increased coverage and integration
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Database resources of the National Center for Biotechnology Information
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SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates
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