Tag: prokaryotic genome


Found 70 sources
Source Match ReputationScore*

The UCSC Archaeal Genome Browser


The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, ...
100%

Pseudomonas Genome DB


The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.
91%

Integrated Microbial Genomes And Microbiomes


The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...
83%

Insertion Sequence Finder


This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequence ...
81%

Microbial Genome Annotation & Analysis Platform


MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and m ...
75%

Virulence Factor Database


VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).
74%

IMG Genomes


Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here we present the 3rd version of IMG/VR, composed of 18,373 cultivated and 2,314,329 uncultivated viral genomes (UViGs), n ...
73%

Database of Bacterial Exotoxins for Human


DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.
71%

GeneDB


GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed ...
64%

HAMAP database of microbial protein families


HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is appli ...
64%

MicrobesOnline


A suite of Web-based tools for comparative genomics
63%

Integrative and Conjugative Elements in Bacteria


A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database ...
60%

CoryneRegNet 6.0 - Corynebacterial Regulation Network


Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.
60%

TADB


Type II Toxin-Antitoxin loci in bacteria and archaea
58%

Prokaryotic Operon DataBase


The Prokaryotic Operon DataBase (ProOpDB) constitutes one of the most precise and complete repository of operon predictions in our days. Using our novel and highly accurate operon algorithm, we have predicted the operon structures of more than 1,200 ...
58%

ProPortal


ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. They provide a source of cross-referenced data across multiple scales of biological organization—from the genome to ...
58%

SubtiWiki


Collaborative resource for the Bacillus community.
55%

Chlamydiae Database


ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using a ...
55%

Effective


Predicted secreted bacterial proteins
54%

MolliGen


Genomic data on mollicutes
53%

Type IV Secretion system Resource


A web-based bacterial type IV secretion system resource for type IV secretion systems (T4SSs) and cognate effectors in bacteria.
52%

ODB - Operon database


ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 ...
50%

EcoliWiki: A Wiki-based community resource for Escherichia coli


EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.
49%

PSSRdb


Polymorphic Simple Sequence Repeats Database
47%

E. coli K antigen 3-dimensional structure database


EK3D - an E. coli K antigen 3-dimensional structure database is a repository of 72 E. coli K antigens that provides information about the sugar composition, epimeric & enantiomeric forms and linkages between the sugar monomers.
47%

HGTree


The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2,472 completely sequenced prokaryotic genomes. HGT detection is based on an explicit evolutionary model of tree reconstruction and relies on evaluating ...
41%

TBDB


Stanford Tuberculosis Database
41%

WDCM


World Data Center of Microorganisms collections
41%

MG-RAST


Data portal for the processing, analyzing, sharing and disseminating of metagenomic data sets
41%

HEG-DB


Predicted highly expressed genes in prokaryotic genomes
38%

Colibri


E. coli genome database at Institut Pasteur
38%

BuchneraBase


Genome of the pea aphid symbiont Buchnera sp. APS
38%

PortEco


Escherichia coli K-12 knowledgebase portal
38%

HPMCD


Human Pan-Microbial Communities Database
38%

DESM


Microbial knowledge exploration systems
38%

AlterORF


Database of alternate open reading frames
38%

Strepto_DB


Database for comparative genome analysis of 15 strains of the genus Streptococcus
38%

antiSMASH


antibiotics and Secondary Metabolite Analysis SHell
38%

coliBASE


A database for E. coli, Salmonella and Shigella
38%

SporeWeb


Regulatory pathways during the sporulation cycle of Bacillus subtilis
38%

Essential genes in E. coli


First results of an E. coli gene deletion project
38%

GenoBase


Escherichia coli K-12 in-frame, single-gene knockout mutants
38%

CauloBrowser


Cell cycle program of Caulobacter crescentus
38%

BSORF - Bacillus subtilis Open Reading Frames


Bacillus subtilis genome database at Kyoto U.
38%

CMGSDB


Computational models for gene silencing in C. elegans
38%

[email protected]


Microarray datasets for microbial gene expression
38%

PEC - Profiling of E. coli Chromosome


Comprehensive database on E. coli genome
38%

HoPaCI-DB


The Host-Pathogen Interaction Database of Pseudomonas aeruginosa and Coxiella spp.
38%

CCDB - The CyberCell Database


E. coli database at U. Alberta
38%

meta.MicrobesOnline


A suite of Web-based comparative genomic tools for metagenome analysis
38%

IMG-ABC


Atlas of Biosynthetic gene Clusters for secondary metabolites
38%

DEG - Database of Essential Genes


Database of essential genes from bacteria and yeast
38%

ASAP - A Systematic Annotation Package


Community analysis of E. coli and related genomes
38%

GenomeAtlas


The GenomeAtlas Database contains information about sequenced microbial genomes, including chromosome maps which visualise various DNA structural properties as colour-coded lanes. The genomes are organised in the three "SuperKingdoms" (Bacteria, Arch ...
38%

SYSTOMONAS


SYSTOMONAS (SYSTems biology of pseudOMONAS, http://www.systomonas.de) is a database on pseudomonads providing data and tools on metabolic network reconstruction, gene-regulatory networks, visualization of genomic structures or metabolic pathways, com ...
38%

Comparative Genometrics


The ever increasing rate at which whole genome sequences are becoming accessible to the scientific community has created an urgent need for tools enabling comparison of chromosomes of different species. We have applied biometric methods to available ...
38%

PAIDB - Pathogenicity Island Database


The pathogenicity island database (PAIDB; http://www.gem.re.kr/paidb) is a comprehensive relational database of all the reported pathogenicity islands (PAIs) and potential PAI regions which were predicted by a method that combines feature-based analy ...
38%

SIDDBase


SIDDBASE (http://www.genomecenter.ucdavis.edu/benham/siddbase) is a database of stress induced DNA destabilization (SIDD) properties of various complete microbial genomes. SIDD sites are locations in genomic DNA which are predicted to become suscepti ...
38%

MtbRegList


MtbRegList is a database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain predicted and characterized regulatory DNA motifs cross-referenced with corresponding transcription fac ...
38%

HGT-DB, Horizontal Gene Transfer-DataBase


The HGT-DB is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that ge ...
38%

LEGER


The Proteome database LEGER (http://leger2.gbf.de/cgi-bin/expLeger.pl) was developed to support functional genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotati ...
38%

MGAN


The Microbial Genome Annotation Network (MGAN) is collaborating with the Genomics Education National Initiative (GENI), Dr. Cheryl Kerfeld (University of California - Berkley, CA) and Dr. Roy Welch (Syracuse University, NY) to provide authentic and i ...
38%

ShiBase


ShiBASE (http://www.mgc.ac.cn/ShiBASE/) is a freely accessible online resource that is focused on the comparative genomics of Shigella. ShiBASE is able to summarize large volumes of genomic sequence and comparative genomic data in a visually intuitiv ...
38%

LeptoList


LeptoList is the reference database dedicated to the genome of Leptospira interrogans serovar Lai, the paradigm of leptospirosis causative agents (1). It has been developed as a spin-off of the B. subtilis genome project (2), GenoList provides a data ...
38%

FARME DB


Antibiotic resistance (AR) is a major global public health threat but little is known about the relationship between AR genes present in the environment and genomic sequences derived from clinical antibiotic resistant isolates. FARMEDB is a database ...
38%

PATRIC, the bacterial bioinformatics database and analysis resource


The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original NIAID-funded BRCs[1,2], PATRIC provides researchers with an online resou ...
38%

RegTransBase


RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory pro ...
38%

ARDB


The treatment of infections is increasingly compromised by the ability of bacteria to develop resistance to antibiotics through mutations or through the acquisition of resistance genes. Antibiotic resistance genes also have the potential to be used f ...
38%

MvirDB


MvirDB (http://mvirdb.llnl.gov/) is a microbial data warehouse of protein toxins, virulence factors, and antibiotic resistance genes for bio-defense applications. MvirDB integrates all publicly available, organized sequence data for protein toxins, v ...
38%

ATGC


The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independen ...
38%

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