SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology
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June 2012
Bacterial Carbohydrate Structure Database 3: Principles and Realization
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December 2010
Genome annotation: from sequence to biology
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July 2001
The future of biocuration
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September 2008
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
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December 2011
Sequencing technologies — the next generation
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December 2009
Phagocytosis-like cell engulfment by a planctomycete bacterium
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December 2019
Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum
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March 2021
Environmental dissemination of pathogenic Listeria monocytogenes in flowing surface waters in Switzerland
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April 2021
Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)
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September 2014
Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)
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September 2014
BuchneraBASE: a post-genomic resource for Buchnera sp. APS
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January 2006
EcoProDB: the Escherichia coli protein database
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July 2007
Prokka: rapid prokaryotic genome annotation
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March 2014
tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis
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January 2014
MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes
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January 2014
PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification
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January 2014
yStreX: yeast stress expression database
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January 2014
MetaProx: the database of metagenomic proximons
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January 2014
DEOP: a database on osmoprotectants and associated pathways
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January 2014
VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets
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January 2014
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics
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January 2014
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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September 1997
Database resources of the National Center for Biotechnology Information
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October 2020
The TIGRFAMs database of protein families
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January 2003
BacMap: an interactive picture atlas of annotated bacterial genomes
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December 2004
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
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September 2005
CryptoDB: a Cryptosporidium bioinformatics resource update
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January 2006
Database resources of the National Center for Biotechnology Information
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January 2006
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data
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January 2006
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
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January 2007
Bacteriome.org an integrated protein interaction database for E. coli
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December 2007
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
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October 2007
xBASE2: a comprehensive resource for comparative bacterial genomics
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December 2007
ToxoDB: an integrated Toxoplasma gondii database resource
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December 2007
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
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January 2009
TB database: an integrated platform for tuberculosis research
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January 2009
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes
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January 2009
PlasmoDB: a functional genomic database for malaria parasites
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January 2009
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets
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November 2009
TriTrypDB: a functional genomic resource for the Trypanosomatidae
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October 2009
The comprehensive microbial resource
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November 2009
MicrobesOnline: an integrated portal for comparative and functional genomics
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November 2009
The MiST2 database: a comprehensive genomics resource on microbial signal transduction
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November 2009
EuPathDB: a portal to eukaryotic pathogen databases
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November 2009
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species
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October 2010
PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea
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November 2010
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
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November 2010
OMPdb: a database of -barrel outer membrane proteins from Gram-negative bacteria
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October 2010
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
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October 2010
WebGeSTer DB—a transcription terminator database
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November 2010
ProOpDB: Prokaryotic Operon DataBase
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November 2011
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage
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November 2011
Saccharomyces Genome Database: the genomics resource of budding yeast
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November 2011
GeneDB--an annotation database for pathogens
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November 2011
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
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November 2011
VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA
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December 2011
The NCBI Taxonomy database
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December 2011
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
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October 2011
The sequence read archive: explosive growth of sequencing data
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October 2011
ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins
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October 2011
FungiDB: an integrated functional genomics database for fungi
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November 2011
HBVdb: a knowledge database for Hepatitis B Virus
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November 2012
EcoCyc: fusing model organism databases with systems biology
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November 2012
CyanoLyase: a database of phycobilin lyase sequences, motifs and functions
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November 2012
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
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November 2012
WholeCellKB: model organism databases for comprehensive whole-cell models
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November 2012
Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides
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November 2012
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates
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November 2012
Database resources of the National Center for Biotechnology Information
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November 2012
NCBI GEO: archive for functional genomics data sets—update
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November 2012
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
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November 2012
GenBank
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November 2012
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
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November 2012
metaMicrobesOnline: phylogenomic analysis of microbial communities
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November 2012
ViralZone: recent updates to the virus knowledge resource
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November 2012
EcoGene 3.0
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November 2012
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis
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November 2012
SecReT4: a web-based bacterial type IV secretion system resource
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November 2012
StreptomeDB: a resource for natural compounds isolated from Streptomyces species
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November 2012
The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis
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October 2012
DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes
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October 2012
ECMDB: The E. coli Metabolome Database
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October 2012
ClusterMine360: a database of microbial PKS/NRPS biosynthesis
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October 2012
Subti Wiki–a database for the model organism Bacillus subtilis that links pathway, interaction and expression information
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October 2013
SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis
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October 2013
BacDive—the Bacterial Diversity Metadatabase
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November 2013
Data, information, knowledge and principle: back to metabolism in KEGG
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November 2013
MetaRef: a pan-genomic database for comparative and community microbial genomics
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November 2013
POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes
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November 2013
The Transporter Classification Database
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November 2013
PATRIC, the bacterial bioinformatics database and analysis resource
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November 2013
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
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November 2013
LPSN—list of prokaryotic names with standing in nomenclature
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November 2013
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
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November 2013
CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes
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November 2013
The carbohydrate-active enzymes database (CAZy) in 2013
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November 2013
Network portal: a database for storage, analysis and visualization of biological networks
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November 2013
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools
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November 2013
The European Bioinformatics Institute’s data resources 2014
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November 2013
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
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November 2013
Pfam: the protein families database
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November 2013
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
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November 2013
SCOP2 prototype: a new approach to protein structure mining
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November 2013
Ribosomal Database Project: data and tools for high throughput rRNA analysis
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November 2013
mVOC: a database of microbial volatiles
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December 2013
BacMet: antibacterial biocide and metal resistance genes database
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December 2013
Virus Variation Resource—recent updates and future directions
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December 2013
IMG/M 4 version of the integrated metagenome comparative analysis system
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October 2013
HoPaCI-DB: host- Pseudomonas and Coxiella interaction database
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October 2013
EBI metagenomics—a new resource for the analysis and archiving of metagenomic data
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October 2013
IMG 4 version of the integrated microbial genomes comparative analysis system
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October 2013
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data
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November 2014
GenoBase: comprehensive resource database of Escherichia coli K-12
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November 2014
Gene Ontology Consortium: going forward
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January 2014
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
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November 2014
The BioGRID interaction database: 2015 update
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November 2014
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
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November 2014
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
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November 2014
CDD: NCBI's conserved domain database
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November 2014
Expanded microbial genome coverage and improved protein family annotation in the COG database
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November 2014
The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection
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January 2015
The InterPro protein families database: the classification resource after 15 years
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November 2014
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus
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September 2014
CATH: comprehensive structural and functional annotations for genome sequences
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October 2014
SMART: recent updates, new developments and status in 2015
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October 2014
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
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October 2014
P2CS: updates of the prokaryotic two-component systems database
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October 2014
Database resources of the National Center for Biotechnology Information
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November 2018
SecReT6: a web-based resource for type VI secretion systems found in bacteria: Genomics update
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July 2015
ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes: ABCdb: transporter repertoires
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March 2006
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal
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May 2015
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal
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May 2015
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
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February 2021
VetBact – culturing bacteriological knowledge for veterinarians
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February 2014
VibrioBase: A Model for Next-Generation Genome and Annotation Database Development
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January 2014
BIGSdb: Scalable analysis of bacterial genome variation at the population level
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December 2010
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
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June 2012
T3DB: an integrated database for bacterial type III secretion system
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January 2012
DBSecSys: a database of Burkholderia mallei secretion systems
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January 2014
The COG database: an updated version includes eukaryotes
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January 2003
RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
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January 2013
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
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January 2013
Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources
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January 2013
Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology
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January 2014
HelicoBase: a Helicobacter genomic resource and analysis platform
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January 2014
SAMMD: Staphylococcus aureus Microarray Meta-Database
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January 2007
AtlasT4SS: A curated database for type IV secretion systems
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January 2012
Submission of Microarray Data to Public Repositories
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August 2004
CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips
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January 2014
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species
journal
June 2014
GeneDB--an annotation database for pathogens.
text
January 2012
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species
text
January 2014
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
text
January 2013
SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates
text
January 2012
BacMap: An interactive picture atlas of annotated bacterial genomes
M. J., Stothard, P. ; Van Domselaar, G. ; Cruz, J. ; Wishart, D. S. ; Shrivistava, S. ; Guo, A. C. ; O'Neill, B. ; Ellison,
University of Alberta Libraries
https://doi.org/10.7939/r3sz8p
text
January 2005