Tag: prokaryotic genome

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, ...

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.

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 ...

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 ...

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

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 ...

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.

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 ...

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 ...

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 ...

A suite of Web-based tools for comparative genomics

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 ...

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

Collaborative resource for the Bacillus community.

Type II Toxin-Antitoxin loci in bacteria and archaea

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 ...

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 ...

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 ...

Predicted secreted bacterial proteins

Genomic data on mollicutes

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

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 ...

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

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.

Polymorphic Simple Sequence Repeats Database

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 ...

World Data Center of Microorganisms collections

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

Stanford Tuberculosis Database

Predicted highly expressed genes in prokaryotic genomes

E. coli genome database at Institut Pasteur

Genome of the pea aphid symbiont Buchnera sp. APS

Escherichia coli K-12 knowledgebase portal

Human Pan-Microbial Communities Database

Microbial knowledge exploration systems

Database of alternate open reading frames

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

antibiotics and Secondary Metabolite Analysis SHell

A database for E. coli, Salmonella and Shigella

Regulatory pathways during the sporulation cycle of Bacillus subtilis

First results of an E. coli gene deletion project

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

Cell cycle program of Caulobacter crescentus

Bacillus subtilis genome database at Kyoto U.

Computational models for gene silencing in C. elegans

Microarray datasets for microbial gene expression

Comprehensive database on E. coli genome

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

E. coli database at U. Alberta

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

Atlas of Biosynthetic gene Clusters for secondary metabolites

Database of essential genes from bacteria and yeast

Community analysis of E. coli and related genomes

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...