List of Database Records  (records : )

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Database maintenance site: The Federal Research Center Institute of Cytology and Genetics Lab, Novosibirsk State University
Organism(s) covered: Anopheles gambiae | Ascaris suum | Bos taurus | Caenorhabditis elegans | Canis familiaris | ...
Description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon st... Show Details...
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Database maintenance site: McDonnell Genome Institute at Washington University School of Medicine, Genome Technology Access Center, Department of Genetics, Washington University School of Medicine
Organism(s) covered: Ancylostoma caninum | Ancylostoma ceylanicum | Ancylostoma duodenale | Ascaris suum | Brugia malayi | ...
Description: Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a componen... Show Details...
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Database maintenance site:
Organism(s) covered: Metazoa | Placozoa
Description: MitoZoa is a specialized database collecting complete and nearly-complete (longer than 7 kb) mtDNA entries of metazoan species, excluding Placozoa. MitoZoa contains curated entr... Show Details...
Database maintenance site: Columbia University
Organism(s) covered: Homo sapiens | Mus musculus
Description: This resource details DNA methylation profiles in human and mouse brain. This database includes genome-wide DNA methylation profiles for human and mouse brains. The DNA methylat... Show Details...
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Inactive
(Over 14 days)
Integrated Pathway Analysis and Visualization System:  IPAVS
Database maintenance site: Systems Biology Laboratory of Gwangju Institute of Science and Technology, Department of Life Sciences
Organism(s) covered: Homo sapiens
Description: iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provide... Show Details...
Database maintenance site: University of Hong Kong
Organism(s) covered: Homo sapiens
Description: GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications Show Details...
Database maintenance site: Evolution of Protein Structure and Function Group, Biomolecular Modelling and Design Division, Bioinformatics Institute
Organism(s) covered: Vertebrata
Description: Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins b... Show Details...
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Database maintenance site: Institute for Microbial Technology
Organism(s) covered: All
Description: ccPDB (Compilation and Creation of datasets from PDB) is a collection of commonly used data sets for structural or functional annotation of proteins. There are numerous datasets... Show Details...
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Database maintenance site: Wishart Lab, University of Alberta
Organism(s) covered: Archaea | Bacteria
Description: BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial g... Show Details...
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Database maintenance site: Mayo Clinic
Organism(s) covered: Danio rerio
Description: Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage ... Show Details...
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Database maintenance site: BIOTEC (The Biotechnology Center, Technische Universitat Dresden), EMBO (European Molecular Biology Organization), University of Copenhagen
Organism(s) covered: All
Description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experim... Show Details...
Database maintenance site: KOBIC(Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)
Organism(s) covered: All
Description: The STAP database contains refined versions of the NMR structures deposited in PDB. These refinements have been performed using statistical torsion angle potential and structura... Show Details...
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Database maintenance site: Switch Laboratory
Organism(s) covered: Homo sapiens
Description: SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and... Show Details...
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Database maintenance site: Jurisica Lab, Ontario Cancer Institute
Organism(s) covered: All
Description: SCRIPDB is a chemical structure database designed to make patent metadata accessible. We index public-domain chemical information contained in U.S. patents, and provide the full... Show Details...
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Database maintenance site: Yale University, Yale University School of Medicine
Organism(s) covered: All
Description: ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. ModelDB is tightly coupled with NeuronDB. Models can be coded i... Show Details...
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Database maintenance site:
Organism(s) covered: All
Description: RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that co... Show Details...
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Database maintenance site: SIB (Swiss Institute of Bioinformatics)
Organism(s) covered: All
Description: Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic net... Show Details...
Database maintenance site: School of Computer Science and Engineering, The Hebrew University of Jerusalem
Organism(s) covered: All
Description: This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, ... Show Details...
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Database maintenance site: Cell Networks, University of Heidelberg
Organism(s) covered: All
Description: Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight. Show Details...
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Database maintenance site: New England Biolabs
Organism(s) covered: All
Description: Polbase is an open and searchable database providing information from published and unpublished sources on the biochemical, genetic, and structural information of DNA polymerases. Show Details...
Database maintenance site: The Abagyan Lab UC San Diego, UCSD (University of California San Diego)
Organism(s) covered: All
Description: The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank... Show Details...
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Closed
PLEXdb
Database maintenance site: USDA-ARS (Agricultural Research Service of the US Department of Agriculture), Iowa State University
Organism(s) covered: Fungi | Nematoda | Oomycetes | Sinorhizobium meliloti | Viridiplantae
Description: PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information wareh... Show Details...
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Database maintenance site: Ming Chen's Lab, Zhejiang University
Organism(s) covered: Viridiplantae
Description: Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. Pl... Show Details...
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Inactive
(Over 14 days)
Plantmetabolomics.org
Database maintenance site: Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology (BBMB), Iowa State University
Organism(s) covered: Arabidopsis thaliana
Description: Arabidopsis metabolomics database which provides researchers with resources to investigate the function of genes and metabolites. Show Details...
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Database maintenance site:
Organism(s) covered: Caenorhabditis elegans | Drosophila melanogaster | Homo sapiens | Mus musculus | Rattus norvegicus | ...
Description: The Protein Interaction Network Analysis (PINA)- is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It in... Show Details...
Database maintenance site: Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto
Organism(s) covered: Saccharomyces cerevisiae
Description: PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mu... Show Details...
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Database maintenance site: MGAN (Microbial Genome Annotation Network)
Organism(s) covered: Bacteria
Description: GENI-ACT is a resource that allows the research community to collaboratively annotate bacterial genomes. Changes can be suggested to existing genomes and these alterations can b... Show Details...
Database maintenance site: Bioinformatics and ECCPS bioinformatics service group, Max Planck Institute for Heart and Lung Research
Organism(s) covered: Notophthalmus viridescens
Description: A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platfo... Show Details...
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Database maintenance site: Gautheret Lab, Institute for Integrative Biology of the Cell
Organism(s) covered: Archaea | Bacteria
Description: NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be vi... Show Details...
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Database maintenance site: The Jackson Laboratory, Bar Harbor
Organism(s) covered: Mus musculus
Description: Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are... Show Details...
Database maintenance site: LBNL (Lawrence Berkeley National Laboratory), InterMine, System Biology Centre
Organism(s) covered: Caenorhabditis elegans | Drosophila ananassae | Drosophila melanogaster | Drosophila mojavensis | Drosophila pseudoobscura | ...
Description: modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser. Show Details...
Database maintenance site: MBU (MRC Mitochondrial Biology Unit, Cambridge, UK)
Organism(s) covered: Eukaryota
Description: MitoMiner is an integrated data warehouse of mammalian localisation evidence, phenotypes and diseases. This data has been integrated to allow the creation of sophisticated data ... Show Details...
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Database maintenance site: ELIXIR, Wellcome Genome Campus, SIB (Swiss Institute of Bioinformatics)
Organism(s) covered: All
Description: The core of the Registry is a catalogue of data collections (corresponding to e.g. controlled vocabularies, databases), their URIs and the corresponding physical URLs (or resour... Show Details...
Database maintenance site: Wellcome Sanger Institute
Organism(s) covered: Arabidopsis thaliana
Description: mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable ... Show Details...
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Database maintenance site: IIT Kanpur (Indian Institute of Technology Kanpur)
Organism(s) covered: All
Description: This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the c... Show Details...
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Database maintenance site: Department of Biology, University of Rome Tor Vergata
Organism(s) covered: All
Description: MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. As of September 2013, This resource uses the IntAct... Show Details...
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Database maintenance site: UZH Chemistry (Department of Chemistry, University of Zurich)
Organism(s) covered: All
Description: MINAS contains the exact geometric information on the first and second-shell coordinating ligands of every metal ion present in nucleic acid structures that are deposited in the... Show Details...
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Inactive
(Over 14 days)
Mimotope Database:  MimoDB
Database maintenance site: HLAB (Huang's Lab)
Organism(s) covered: All
Description: Mimotope database, active site-mimicking peptides selected from phage-display libraries. It is a database which stores information on peptides that have been selected from rando... Show Details...
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Database maintenance site: IPK (Leibniz Institute of Plant Genetics and Crop Plant Research)
Organism(s) covered: Arabidopsis thaliana | Beta vulgaris | Brassica napus | Hordeum vulgare | Medicago truncatula | ...
Description: The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated inform... Show Details...
Database maintenance site: University of Florida
Organism(s) covered: Drosophila melanogaster | Homo sapiens | Mus musculus
Description: This resource provides information primarily on the upstream non-coding sequence data of genes in 3 genomes which gives insight into the transcription factors binding sites (TFB... Show Details...
Database maintenance site: Zhao Bioinformatics Laboratory
Organism(s) covered: Lotus japonicus | Medicago truncatula
Description: The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes. Show Details...
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Database maintenance site: CNRS (The National Centre for Scientific Research)
Organism(s) covered: All
Description: Evolution of protein-protein Interfaces InterEvol is a resource for researchers to investigate the structural interaction of protein molecules and sequences using a variety of t... Show Details...
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Database maintenance site: State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University
Organism(s) covered: Bacteria
Description: A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature,... Show Details...
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Database maintenance site: Center for Computational Biology and Bioinformatics and College of Engineering (CCBB), Koc University (KU)
Organism(s) covered: All
Description: Database of interaction Hotspots across the proteome. Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the inter... Show Details...
Database maintenance site: University of Bari
Organism(s) covered: Homo sapiens
Description: HmtDB is an open resource created to support population genetics and mitochondrial disease studies. The database hosts human mitochondrial genome sequences annotated with popula... Show Details...
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Database maintenance site: ACTREC (Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre)
Organism(s) covered: Homo sapiens
Description: HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-transl... Show Details...
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Database maintenance site:
Organism(s) covered: Homo sapiens
Description: HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD info... Show Details...
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Database maintenance site: SIB (Swiss Institute of Bioinformatics)
Organism(s) covered: All
Description: The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions. Gene expression data is re-analysed in-house to ... Show Details...
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Database maintenance site:
Organism(s) covered: All
Description: A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function. Show Details...
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Database maintenance site: CBIL (Computational Biology and Informatics Laboratory, University of Pennsylvania), Center for Tropical & Emerging Global Diseases, University of Georgia, United States Department of Health and Human Services
Organism(s) covered: Fungi | Oomycetes
Description: FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experiment... Show Details...