3D-Genomics
(Imperial College London) |
- database that contains protein structure and function annotation across different genomes
- current focus:
- identification of transmembrane regions, coiled-coils, low complexity regions, Prosite-patterns, PFAM and SCOP domains, repeats, homologous sequences and secondary structure prediction
- structural information (fold classification) assigned to genome sequences via homology (using BLAST, PSI-BLAST and 3D-PSSM)
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ACLAME - A Classification of Genetic Mobile Elements
(SCMBB) |
- database dedicates to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons
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BacMap - Genome Atlas
(University of Alberta) |
- interactive atlas for exploring bacterial genomes
[Stothard, P.; Van Domselaar, G.; Shrivastava, S.; Guo, A.; O'Neill, B.; Cruz, J.; Ellison, M.; Wishart, D.S.; Nucleic Acids Res. 2005, 33, D317-D320. BacMap: an interactive picture atlas of annotated bacterial genomes.]
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Bio-Dictionary-based Annotations of Complete Genomes
(IBM) |
- annotations of complete genomes
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CAZy - Carbohydrate-Active Enzymes
(AFMB-CNRS) |
- database describes families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds
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CMR Genomes Arranged by Taxonomy
(TIGR) |
- general properties, information and chromosomal displays of Spirochaetes
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CUBIC
(Columbia University Bioinformatics Center) |
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DDBJ - DNA Data Bank of Japan
(National Institute of Genetics) |
- international nucleotide sequence database in collaboration with EBI/EMBL and NCBI/GenBank
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Ensemble Genome Browser
(Ensemble) |
- joint project between EMBL-EBI and the Sanger Institute
- Ensemble Trace Server
- permanent archive for single pass DNA sequencing reads and associated traces and quality values
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Entrez Genome
(NCBI) |
- contains genome data of all three main domains of life - bacteria, archaea, and eukaryota, as well as many viruses and organelles
- genomes represent both completely sequenced organisms and those for which sequencing is in progress
- Borrelia, Leptospira and Treponema genomes
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ERGO™ Bioinformatics Suite
(Integrated Genomics Inc.) |
- genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes
- ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes
- Borrelia, Leptospira and Treponema genomes
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ExPASy Proteomics Server
(Swiss Institute of Bioinformatics) |
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FusionDB
(CNRS) |
- database of bacterial and archaeal gene fusion events - also known as Rosetta stones
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Gene3D
(UCL, University College London) |
- supplementary to the CATH database (protein structure classification)
- contains proteins from complete genomes which have been clustered into protein families and annotated with CATH domains, Pfam domains and functional information from KEGG, GO, COG, Affymetrix and STRINGS
- Borrelia burgdorferi, Leptospira interrogans serovar lai str. 56601 and Treponema pallidum
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GeneQuiz
(EMBL-EBI Cambridge, UK & CNB-CSIS Madrid, Spain) |
- integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases
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genomemine
(Centre for Ecology & Hydrology Oxford, UK) |
- contains published genomes from bacteria, plasmids, organelles, and viruses
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Genome Annotation Browser
(Health Protection Agency, UK) |
- scans the annotation of one of the completed genomes listed at the NCBI site
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Genome Atlas Database
(Center for Biological Sequence Analysis, Technical University of Denmark) |
- DNA structural atlases for complete chromosomes and genomes
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Genome-Tools
(Stanford University & SourceForge) |
- flexible package for genome sequence analysis
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GNN - Genome News Network
(J. Craig Venter Institute) |
- genomes of more than 180 organisms have been sequenced since 1995
- GNN includes descriptions of these organisms and has links to sequencing centers and scientific abstracts
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GTD - Genomic Threading Database
(UCL, University College London) |
- contains structural annotations of proteomes, translated from the genomes of key organisms (GenTHREADER - annotation software)
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GtRNA - The Genomic tRNA Database
(University of California, UCSC RNA Center) |
- contains tRNA identifications made by the program tRNAscan-SE on complete or nearly complete genomes
[Lowe, T.M.; Eddy, S.R.; Nucl. Acids Res. 1997, 25(5), 955-964. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.] [PubMed]
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HGT-DB - Horizontal Gene Transfer Database
(URV, Universitat Rovira i Virgili) |
- 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
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In silico Experiments with Complete Genomes
(University of the Basque Country) |
- different tools for in silico experiments with complete genomes (PCR amplification, ORF search etc.)
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Integr8
(EMBL-EBI) |
- browser for information relating to completed genomes and proteomes, based on data contained in Genome Reviews and the UniProt proteome sets
- provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO
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IslandPath
(Simon Fraser University) |
- aid to the identification of genomic islands, including pathogenicity islands, of potentially horizontally transferred genes
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lsu rRNA Database
(University of Gent) |
- database on the structure of lsu ribosomal subunit RNA (lsu rRNA)
- includes indications of secondary structure elements for each sequence, based on the adopted rRNA secondary structure, which in turn is corroborated by the observation of compensating substitutions in the alignment
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KEGG - Kyoto Encyclopedia of Genes and Genomes
(Kyoto University Bioinformatics Center) |
- bioinformatics ressource (chemical, genomic and pathway information)
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LeptoList
(Pasteur Institute) |
- constructed around a database dedicated to the analysis of the genome of Leptospira interrogans serovar Lai
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Magpie Automated Genomics Project Investigation Environment
(University of Calgary) |
- software package for the automated curation and presentation of DNA and protein sequences
- distills the results of multiple database searches for each sequence (e.g. expressed sequence tags, ESTs) or subsequence (e.g. open reading frames, ORFs, in bacterial genomic DNA) into a summary page that facilitates interpretation of genes' biological roles and origins
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MBGD - Microbial Genome Microsatellite Database
(Field Research Lab, CEH Oxford) |
- information about Borrelia, Leptospira & Treponema
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MEROPS - Peptidase Database
(Wellcome Trust Sanger Institute) |
- information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and proteins that inhibit them
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MGCUD - Microbial Genome Codon Usage Database
(Forsyth Institute & Northeastern University) |
- information about Spirochaetes (Borrelia, Leptospira & Treponema)
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ORALGEN - Oral Pathogen Sequence Databases
(Los Alamos National Laboratory Bioscience Division) |
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PathoGene
(University of Texas Southwestern Medical Center & RCE Region VI Computational Biology Group) |
- web based program designed to locate a user specified coding sequence (CDS) in a microbial, viral, or fungal genome and build primers for it using
- information about Borrelia, Leptospira & Treponema
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PEDANT - Protein Extraction, Description, and Analysis Tool
(MIPS & BioMAX) |
- computational analysis of complete genomic sequences
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PGD - Plasmid Genome Database
(Centre of Ecology and Hydrology-Oxford & Danish Technical University) |
- collate biological and genomic data for all bacterial plasmids in the hopes of enabling rapid, interrogation of both meta- and genomic data
- data maintained includes access to all plasmid genomes, information on core genomic features like number of ORFs, and structural maps (Genome Atlas)
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PIR - Protein Information Resource
(Georgetown University Medical Center, Washington, DC) |
- integrated public bioinformatics resource that supports genomic and proteomic research and scientific studies
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PPD - Proteome Profile Database
(Bioinformatics Institute, Singapore) |
- database on protein length distribution of genomes
- key components:
- classify proteins into groups based on their lengths,
- calculate the percentage change in proteins of a specific length among the chosen organisms, and
- amino acid composition profiles online
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PSORTb
(Brinkman Laboratory, Simon Fraser University) |
- program for bacterial protein subcellular localization prediction
- information for Spirochaetales
(Borrelia burgdorferi B31, Borrelia garinii PB1, Leptospira interrogans serovar Copenhageni str. Fiocruz LI-130 chromosome 1 & 2, Leptospira interrogans serovar laistr. 56601 chromosome 1 & 2, Treponema denticola ATCC 35405, Treponema pallidum subsp. pallidum str. Nichols)
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repairGenes
(Centre for Molecular Biology and Neuroscience, University of Oslo) |
- source of information about DNA repair genes from a set of selected species (coverage of DNA repair genes is not complete)
- raw data about DNA repair genes extracted from the SWISS-PROT database and categorised by using the GO
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rrndb - Ribosomal RNA Operon Copy Number Database
(Michigan State University) |
- information pertaining to the number of rRNA operons contained on the genomes of prokaryotic microorganisms in a phylogenetic context
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STD Sequence Database
(Los Alamos National Laboratory) |
- includes both compilation and analysis of molecular sequence informtaion pertaining to sexually transmitted bacteria and viruses
- dynamic graphics and extended analyses available for all organisms
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Superfamily - HMM Library and Genome Assignments Server
(MRC Laboratory of Molecular Biology, Cambridge & Stanford University, USA) |
- server offers sequence searching, alignments and genome assignments
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Taxonomy Browser Database
(Michigan State University) |
- original data analysis tool for visualizing the taxonomic relationships among the prokaryotes
- relationships are based on the evolutionary distances between the organisms (measured by using the small subunit ribosomal RNA; SSU rRNA)
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Taxonomy Browser Database
(NCBI) |
- collate taxonomic and phylogenetic information
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Treponema Molecular Genetics Server
(University of Texas Medical School, Houston) |
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UniProt - Universal Protein Resource
(EBI) |
- world's most comprehensive catalog of information on proteins
- central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR
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VIMSS Comparative Genomics
(Virtual Institute for Microbial Stress and Survival) |
- VIMSS microbial comparative genomics website is designed specifically to facilitate multi-species comparison
- highlights include the operon and regulon predictions, the multi-species genome browser, the VertiGo gene ontology browser, KEGG metabolic pathway viewer and the Bioinformatics Workbench
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ViruloGenome
(University of Birmingham) |
- web resource allows users to exploit data from complete and incomplete genome sequencing projects (BLAST and PSI-BLAST searches, sequence retrieval and visualisation of genome sequence data)
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Z Curve Database of Genomes
(Tianjin University, China) |
- a graphic representation of genome sequences (unique 3D curve representation for a DNA sequence in the sense that each can be uniquely reconstructed given the other)
- Z curves for Borrelia burgdorferi and Treponema pallidum
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