KRGDB / Korean Reference Genome DB
Aims to furnish users with a comprehensive map of the Korean genomic variants. KRGDB is a genome variants database that contains information from about 622 healthy individuals. It can be useful for studying disease association and population genetics.
Homology Docking Benchmark
Assists users in exploring and solving combined modeling and docking problems. Homology Docking Benchmark provides means to generate large, customized ensembles of potential template structures from the Protein Data Bank (PDB), for the components of target complexes representing hetero-complexes of single domain proteins from the docking benchmark V4. The database can be a starting point for the development and evaluation of any combination of template-based modeling, docking and refinement methods.
BLDB / Beta-Lactamase Database
Gathers sequence information, biochemical and structural data on all the currently known Beta-Lactamase (BL). BLDB is a web-based database that consists of: (i) a list of classes and sub-classes of BLs, with their corresponding BL families, (ii) a table containing all three-dimensional structures of BLs reported in the Protein Data Bank (PDB), (iii) the synthetic mutants described for each enzyme in the literature, with bibliographical information and links to PDB structures and hydrolytic profiles and (iv) a protein- and nucleotide-based BLAST search.
DCA vs. Misfolds
Provides access to data from studies on direct coupling analysis (DCA) ability to differentiate between properly folded and misfolded structures. DCA vs. Misfolds is dedicated to studies on DCA, a method that can assist researchers in studying protein structure.
PodlewskaEtAl2017
Provides access to target-focused combinatorial libraries of new potentially active compounds. The database stores, in the SMILE format, compounds generated using a tool for combinatorial libraries enumeration with optimization of the compound structures using machine learning (ML) methods.
SBDG / Structural Biology Data Grid
Allows users to discover, download and deposit large structural biology datasets. SBDG is a flexible data publication system that allows deposition of a variety of large primary datasets. The database collection is limited to datasets that support journal publications, referred to as primary data. Datasets are stored as sets of experimental metadata (experimenters, sample, collection facility) and associated files and directories comprising the data of interest. SBDG can facilitate integration of the Data Grid with regional projects and preservation of primary diffraction datasets.
Intensification
Provides access to the result of repeat protein domains, obtained from the amplification of population-genetic signal by constructing a motif-based multiple sequence alignment (motif-MSA). Intensification is a resource for annotating variants in 12 protein-protein interactions (PPI) repeat protein domains (RPDs). The database contains data files for ankyrins (ANK), annexins (ANX), armadillos (ARM), cadherin repeats (CA), fibronectin type 2 domains (FN2), fibronectin type 3 domains (FN3), leucine-rich repeats (LRR_TYP), spectrin repeats (SPEC), tetratricopeptide repeats (TPR), ubiquitin-interacting motifs (UIM), WD40 repeats (WD40), and WW domains (WW).
Meta-All
Allows management of several types of information. Meta-All is designed for administration of detailed information about metabolic pathways, including reactions, translocations, substances, pathways, locations and kinetic parameters. It can be installed locally to help biologists and biochemists in their daily research. User can enter own experimental data as well as data sets from other sources such as publications or databases.
SPDBS / SBML-based Biochemical Pathway Database System
Integrates information about biochemical pathway. SPDBS is an online resource that: (1) imports/exports SBML documents; (2) builds networks at different levels of representation starting from the detailed pathway graph; (3) allows dynamic visualization/ simulation of the pathways; (4) predicts the metabolic pathways for a given genome sequence; and (5) integrates the heterogeneous and distributed pathway databases.
IDP4+
Offers an unbiased representation of mutation mention forms. IDP4+ is a corpus composed of three sub-corpora: IDP4, nala_known, and nala_discoveries.
PalmComparomics
Contains the main results of the exploitation of the comparison of a target species (coconut) and a reference species (oil palm) for improving transcriptomic resources. PalmComparomics is a web a resource that also offers several tools for data querying and visual analyses. It provides a BLAST tool allowing the user to align sequences against the coconut polypeptides and contigs. Users retrieve data, including polypeptides and proteins products, gene ontology annotations, and Interpro or Pfam domains of coconut polypeptides.
FlowerNet
Permits analysis of genes involved in anther and pollen development in order to discover new players during development. FlowerNet has broader application in the characterization of all genes associated with aspects of plant reproduction and flowering. The network has been created using 66 Arabidopsis Affymetrix wild-type microarrays from plant reproduction-related experiments, which included flowers, buds, anther/stamen samples, and isolated pollen samples.
OrCGDB / Oral Cancer Gene Database
Reports altered genes in oral cancer. OrCGDB is designed to be optimal for utilization of the information for diagnosis, prognosis and treatment. It has been used to predict the possible role of differentially expressed markers in cell transformation. The database provides the scientist information and external links for the genes involved in oral cancer, interactions between them, and their role in the biology of oral cancer along with clinical relevance.
RRDB / RNA-RNA Docking Benchmark
RRDB is comprehensive and nonredundant RNA-RNA docking benchmark. This dataset was organized into three different groups according to the interface conformational changes between bound and unbound structures: 47 ‘easy’, 38 ‘medium’, and 38 ‘difficult’ targets. This resource is beneficial for the development and improvement of docking algorithms and scoring functions for RNA-RNA interactions.
HoTResDB / Host Transcriptional Response DataBase
Explores relationships and trends in datasets of specific genes of interest. HoTResDB allows visitors to access processed microarray and NGS data from non-human primates’ models of viral hemorrhagic fever to better understand the host transcriptional response. Users with gene IDs or Ensembl identifiers of interest can view the data in several graphical formats and download raw data. Additionally, a keyword search is available to facilitate the general search.
Hereditary Hearing loss Homepage
Provides researchers and clinicians with an overview of the genetics of hereditary hearing impairment. Hereditary Hearing loss Homepage is a database that contains data about localization and identification of genes for monogenic non syndromic hearing impairment, as well as links.
Anti-CRISPRdb
Provides access to data about anti-CRISPR proteins. Anti-CRISPRdb is an online resource that contains more than 400 anti-CRISPR proteins tested by experimental and bioinformatics methods. The database allows users to browse, search, blast, screen, and download data on their anti-CRISPR proteins of interest, as well as sharing data on validated/potential anti-CRISPR proteins with other related scientific communities.
miRCarta
Collects human MicroRNAs (miRNAs) and miRNA candidates. miRCarta is a database developed to provide the information of miRBase as well as more recent data stemming from miRNA predictions. It aims to bridges the gap between established annotations in miRBase and more recent miRNA predictions from publications and the software miRMaster. miRCarta thus contains the miRBase database and additional new miRNA candidates, expression data, updated organisms, and genomes as entry point for miRNA researchers.
REFOLDdb
Provides optimized refolding methods/conditions for each protein. REFOLDdb offers users data on about 1900 experimental methods for refolding more than 1600 proteins. It is searchable by sequence similarity; and equipped with statistics that enables the discovery of trends in refolding techniques. The database contains a diverse cross-section of protein architectures, including extracellular domains, subunits, whole proteins and multiple proteins.
Chironomid DNA Barcode Database
Provides data about chironomid specimen records. Chironomid DNA Barcode Database contains the species name, DNA sequence of the mitochondrial cytochrome c oxidase 1 gene, a collection of details such as date or place, and photos.
International Human Epigenome Consortium Data Portal
Generates and releases reference epigenome maps of normal and disease tissues along with appropriate metadata. IHEC data portal was constructed employing a distributed data model. It navigates the reference epigenomic datasets generated by the consortium. The database allows epigenomic data integration, discovery, visualization, analysis, download, and sharing.
YIO Database / Yamashina Institute for Ornithology Specimen Database
Provides approximately 69 000 bird specimens and includes skins, spread wings, skeletal specimens, spirit specimens, eggs, and nests.
Acytostelium Gene Database
Provides gene models for Acytostelium subglobosum. Acytostelium Gene Database was constructed by combining three sets of gene models, transcript sequences thank to data from cDNA and EST analyses, homology based predictions, and ab initio predictions. It contains more than 12 700 non-redundant protein coding gene generated.
KANPHOS / Kinase-Associated Neural Phospho-Signaling
Provides phosphorylated sites for kinases. KANPHOS offers a tuple of a kinase, its substrate, the extracellular signal for the phosphorylation, and the experimental condition used for the identification. It permits users to search data in three ways: (1) searching for substrates phosphorylated by a specific kinase; (2) searching for kinases phosphorylating a specific protein; and (3) searching for kinases and their target substrates involved in a specific signaling pathway.
ChemTHEATRE / Tractable and Heuristic E-Archive for Traceability and Responsible-care Engagement
Allows sharing and displaying monitoring data of environmental contaminants. ChemTHEATRE aims to make the prediction of global chemical pollution easier in cooperation with external database or other tools. It allows storage of data on chemicals in cooperation with the Environmental Specimen Bank.
J-EDI / JAMSTEC E-library of Deep-sea Images
Offers sea images and dive surveys. J-EDI permits users to build they own library of deep-sea photos and movies.
mitotRNAdb
Offers data about mammalian mitochondrial tRNA sequences. mitotRNAdb allows implementation and validation of algorithms and can process to automated nucleic acid data transfer. It combines tRNA gene sequences and classifies them in two categories: ‘Genomic tRNA Compilation’ and ‘Compilation of tRNA Genes’. The database includes tRNA-like structures (TLSs) encoded in viruses and phages.
ViBrism / Virtual Brain with 3D-ISM
Offers a spatial overview of gene expression patterns of the mouse brain. ViBrism provides more than 172 000 expression maps of transcripts, including coding, non-coding and lncRNAs in the whole context of 3D magnetic resonance (MR) images. The platform hosts a software that allows integrated analysis of 3D gene expression maps and graphs of co-expression networks. It enables the analysis of co-expression gene networks throughout the brain, along with an anatomical overview.
CaPriCo / Captive Primate Collection
Offers specimen information of more than 6 300 captive primates. CaPriCo provides data on skeletal and formalin-preserved specimens of brain, digestive organ and parasite specimens.
e-Foram Stock
Provides e-specimen over computer networks. e-Foram Stock allows users to access to three-dimensional virtual models developed by Tohoku University Museum. The database offers e-specimen based on information of real specimen. It is searchable by generic and specific names, locality and the geological age.
GlycoNMR
Provides nuclear magnetic resonance (NMR) analysis of glycan. GlycoNMR offers data about structure, glycan type, chemical name, coupling constant, chemical shift and other information.
iJGVD / Integrative Japanese Genome Variation Database
Provides allele frequency data for more than 4 000 000 autosomal single nucleotide variants (SNVs). iJGVD contains SNV alleles, genomic positions based on the GRCh37/hg19 coordinates, allele frequencies, the corresponding dbSNP IDs, P values for the Hardy–Weinberg equilibrium test, gene annotations and so on. It provides functions to explore the region surrounding an SNV based on chromosome coordinates. The database can be requested with gene symbol, rsSNP ID, or genomic position.
START / Signal Track Analytical Research Tool
Allows simple integrated analysis of private and commonly-used public signal tracks. START is an online resource that provides a generic way for analyzing a large number of genomic signal tracks. This database contains a web interface that guides users to construct Signal Track Query Language (STQL) queries. It also provides example queries for various types of data analysis.
GMTV / Genome-wide Mycobacterium tuberculosis variation
Gathers information about M. tuberculosis. GMTV includes clinical, epidemiological and microbiological description with genome variations based on whole genome sequencing data. It contains the whole genome sequences of more than 1000 M. tuberculosis isolates with various medical datasets from different regions. Besides, the database allows users to run association analysis between molecular variation and clinical consequences and aims to make easier the epidemiological surveillance of TB and HIV/TB co-infection.
PULDB / Polysaccharide-Utilization Loci DataBase
Compiles information about polysaccharide utilization locus. PULDB provides a repository, part of the CAZy database, for over 3900 PUL predictions in more than 70 species. The database provides the user with the list of all PULs for a given species, or taxonomic group. Searches can be made by species, modules or locus tag. The results provide an interactive visualization with confidence levels which allows users to reverse PUL’s orientation and a table of results which can be reordered to bring similar PULs closer.
CrossCheck
Provides a centralized repository for published datasets. CrossCheck allows users to compare a user-defined list of gene symbols with the software reference database. The database contains over 600000 screen hits from published high-throughput screen datasets and low-throughput published information deposited into NCBI databases, as well as a novel predicted protein kinase substrate database.
BIG / Biological Information Gatherer
Compiles large-scale proteomic and transcriptomic datasets from the NHLBI Epithelial Systems Biology Laboratory and various datasets from other laboratories. BIG provides access to more than 140000 records dealing with kidney physiology. Users can retrieve information by entering an official gene symbol and choose a kidney-structure delimiter. The results provide a uniform information from all indexed databases.
GEE / Gene Expression data Explore
Compiles information from whole-genome epigenetic and microarray data in public databases. GEE retrieves suitable high-throughput functional genomic datasets by making specific queries using eVOC and EFO vocabularies, EDQC system or specific filter conditions. The database contains more than 30000 high-throughput functional genomic datasets from GEO and ArrayExpress. Results are provided for each platform together with sample information.
MOSAIC
Gathers information about mapping chemical-genetic (CG interactions) in yeast. MOSAIC includes CG interaction data, mode-of-action predictions and chemical structural information for characterized and uncharacterized compounds. Searches can be made by CG profiles, gene and bioprocess-level target predictions. This resource can serve as a starting point for discovering new probes with specific modes-of-action or further characterization of novel compounds.
PCAWG / PanCancer Analysis of Whole Genomes
Gathers information about available whole-genome sequencing (WGS) data from The International Cancer Genome Consortium’s (ICGC). PCAWG contains a set of matched whole genome and transcriptome sequencing for over 1,100 samples from more than 20 different cancer. It intends to help in detecting novel cancer-associated genes, investigating about the impact of coding and non-coding mutations on the transcriptome and binding genetic alterations with related molecular transformations.
CSCD / Cancer-Specific CircRNA Database
Gathers information about all type of circRNAs. CSCD compiles RNASeq datasets in cancer and normal samples added to an integrated circRNA database which principally focus on improvement of functional studies about cancer-specific circRNAs. Searches can be made by sample name, gene symbol or circRNA ID. Users can also perform splicing events prediction or detect potential functional regulation and translation of a specific circRNA by using microRNA response elements (MRE) prediction, RNA binding protein and open reading frame (ORF).
ActiveDriverDB
Permits users to visualize genome mutations in gene and protein networks. ActiveDriverDB is a proteo-genomics resource for interpreting human genome variation using post-translational modification (PTM) sites. Novice users can start from example queries of well-annotated genes. Users can also interpret candidate variants from DNA sequencing experiments and compare it with existing public datasets as well as run an automatically analysis of specific variants. Besides, it includes various search options and can generate export tables, upload and publication-quality figures.
Cabbage Looper Database
Provides a combined divers genomic sequencing data. Cabbage Looper Database is a downloadable resource that assembles sequenced and assembled de novo the genome of the cabbage looper, Trichoplusia ni, a common and destructive agricultural pest that feeds on many plants of economic importance. The aim of this resource is to assemble a chromosome-level, high-quality of the T. ni genome.
BioCarian
Allows exploration of biological databases utilizing semantic web methods. BioCarian is a search engine that browses several selected public databases. The databases consist in a sample collection of DNA-level data (dbSNP, GWAS, Ensembl), protein data (UniProt), pathway data (KEGG, Reactome), disease data (OMIM, DisGeNET) and a private database containing viral integration sites in the liver cancer patients. BioCarian can be used to do a primary analysis of data and act as means of an independent, orthogonal verification of an analysis result.
CiAID / Ciona intestinalis Adult In situ hybridization Database
Gathers information about ascidian Ciona juvenile and adult. CiAID contains a body atlas of the Ciona juvenile including morphological and developmental information, photographs, texts, graphs, 3D models constructed by the serial sections, technical tips, 3D-CG models, and links to the corresponding database. Searches can be made, in more than 20000 datasets, by basic search or by advanced search using a combination of results from the basic one.
Gendoo / Gene, Disease Features Ontology-based Overview System
Provides a repository of profiles diseases and genes associated with related drugs, biological phenomena and anatomy described with MeSH vocabulary. Gendoo includes more than 1700000 associations. The database allows users to visualize associations between OMIM entries and relevant MeSH terms and compare different features. Searches can be made by OMIM IDs, OMIM titles, Entrez Gene IDs, gene names or MeSH terms.
RefExA / Reference database for gene Expression Analysis
Provides a repository that allows users to search and compare gene expression profiles from several human tissues, organs and cells. RefExA also authorizes to make comparisons between sets thanks to an expression panel view and a graph module both including a section dealing with gene annotation. Searches can be made by multiple terms such as Genbank accession or gene symbol.
Database of Aquatic Organisms
Provides a repository that centralizes information about aquatic life living. The database of Aquatic Organism is a manually curated database, open to volunteers’ submission. The content is organized around the “specie” concept, based on the NCBI’ classification. It is composed of materials such as creature information accompanied by figures and photographs, DNA and stock information.
BISMaL / Biological Information System for Marine Life
Gathers information about marine biodiversity. BISMaL contains a wide range of data including description on taxonomy, photographs, distribution map, videos and references for each species. The database also allows users to explore two specific components: occurrence records, which gathers information about how organisms were observed and collected; and taxon metadata, which provides taxonomic groups information by using the Linnaean classification system.
The NAISTrap database
Compiles the nucleotide sequences of about 900 cDNA fragments derived from the mouse trapped genes candidates. The NAISTrap database provides a description of the genes for each embryonic stem (ES) cell clone including features such as gene identity, or deleted regions symbol.
KAIKOcDNA
Provides a repository for silkworm genome information for functional and applied genomics, including data from KAIKO2DDB of proteome data, Bombyx trap database for transgene and reporter data. KAIKOcDNA compiles genomic sequences, map information and expressed sequence tags (EST) data. The database makes available 4 map viewers: gene viewer, sequence search, keyword and position search systems. Results can be visualized at the level of nucleotide sequence, gene, scaffold and chromosome.
RGRC / Rice Genome Resource Center
Concentrates information about structure and function of the rice genome. RGRC manages resources and materials generated by the Rice Genome Research Project such as large-scale analysis of all expressed genes in rice, construction of a genetic map or mutant panel project. The structure delivers access to rice insertion mutant lines and material for genetics analysis on demand. The website includes a price list for each required elements.
The Multi-Dimensional Human Embryo
Improves the distribution of human embryological image data. The Multi-Dimensional Human Embryo intends to collect 3D magnetic resonance data of normal human embryos from Carnegie stages 10–23. It produces a series of images of each embryo in three principal imaging planes (transverse, coronal, and sagittal), a series of volume-rendered images to represent surface features of each whole embryo, and a series of images to demonstrate time-lapse growth of the human embryo.
ITIS / Integrated Taxonomic Information System
Provides a repository for taxonomic data. ITIS is an authoritative source, result of a partnership of federal US agencies, of currently used names of all biological taxa. It proposes guidelines and sets of standards to facilitate comparisons between biodiversity datasets and satisfy their mutual needs for scientifically credible taxonomic information.
TMIG-2DPage / Tokyo Metropolitan Institute of Gerontology two-dimensional gel protein database
Gathers information about proteomic analysis of molecular mechanisms of aging and age-dependent cell dysfunction. TMIG-2DPage compiles PDLdependent protein variation of individual spot proteins. The database gives access to their physico-chemical properties, information about the spot identity, references of papers that dealt with the spot proteins and details of the age-related alteration of its relative abundance during aging.
EPFDB / Entomopathogenic Fungi Database
Aims to furnish a repository for fungi’s characterization by collecting images. EPFDB aims to heap micro photographs from volunteers to constitute a photograph library about entomopathogenic fungi specimens. The collection is available for consultation by alphabetical order, taxonomy, list of species, hosts or synonyms.
ELKUType
Compiles type specimens conserved in the Entomological Laboratory of Kyushu University (Japan). The ELKUType focuses on holotypes. Searches can be made by a simple logical formula or by a combination. Each record is composed of 17 items, such as scientific name, Japanese name, order, family, source of the original description, or existence of paratypes.
HANABACHI
Provides a repository for detailed information about Japanese bees. HANABACHI inventories The Kyushu University Museum collection and provides detailed record about each species. Each entry is composed of 16 items such as visiting or associated flowers, synonymy, or parasites. Besides, the database also contains several images - of the whole body, the head in frontal view, the mesoscutum, the propodeum, and the metasomal terga for each sex - which can be enlarged to examine detailed morphology.
CicerTransDB / Cicer Transcription Factor Database
Contains transcription factors (TFs) of chickpea discovered by the process of cataloguing domains of chickpea gene-products. CicerTransDB provides about 1100 chickpea TFs grouped into 47 separate families. It offers a web interface allowing to query various databases such as InterProScan, PlantCare and many more. This database permits users to visualize and cross-search chickpea TFs aiding to the study of chickpea signalling geometrically.
SpaServer Database
Collates and harmonizes data from various geographic regions. SpaServer is a database of Staphylococcus aureus, a major human pathogen causing skin and tissue infections, pneumonia, septicemia, and device-associated infections. This online resource provides spa-repeat sequences and the -types that can be downloaded. Chromatograms of new spa-repeats and/or -types can be submitted online for inclusion into the reference database.
XenMine
Provides a platform to query publicly available Xenopus genomic data. XenMine permits the access of user-friendly tools for further hypothesis generation. This online resource (i) recovers genomic sequence for given features in the genome, (ii) allows querying and visualization of multiple ChIP-Seq experiments, (iii) gives a platform for simple list analysis and (iv) allows users to easily manipulate template queries for their own specific needs.
Actinobase
Collects information about the diversity and functional analysis of salt tolerant alkaliphilic actinomycetes. Actinobase compiles data from over 40 alkaliphilic actinomycetes including respect to habitat, taxonomy, genus, Gram reaction, biochemical tests or sugar utilization. The database includes the collection of 16S rRNA and protein sequences, several sequence alignment analysis and phylograms created for the available sequences.
CAMPS / Computational Analysis of the Membrane Protein Space
Provides an automatic classification approach of helical membrane proteins including at least three transmembrane helices. CAMPS allows users to browse prokaryotic, eukaryotic, and viral genomes. It offers a large-scale classification not restricted to proteins with known structure. The database includes eukaryotic and viral membrane proteins in the classification approach as well as higher-order hidden Markov models (HMM) and loop length patterns as an additional fold determinant.
SNObase / S-Nitros(yl)ation database
Gathers literature about single-target S-nitrosation and S-nitrosoproteomic research from PubMed. SNObase is a manually curated database that collects information about S-nitrosation target, site, biological model, related disease, trends of S-nitrosation level and manner of regulation in protein function. Searches can be made by several queries as well as description, gene symbol, SNObase ID or Related pathophysiological process.
QuAD / Quantitative Assay Database
Provides a resource for the analysis of proteins implicated in tumorigenesis and cancer progression. QuAD is an online resource for investigators who want to share assays and to enable multiplexed measurements for exploring hypotheses in systems biology. It also enables portability of Liquid Chromatography-Mass spectrometry multiple reaction (LC-MRM) method development and dispersal of the experimental designs and techniques.
HOMER / Human Organ-specific Molecular Electronic Repository
Analyzes, identifies, and characterizes organ-specific molecules in association with disease-organ and disease-protein relationships. HOMER is a comprehensive database covering about 22,600 proteins, 52 organs, and 4,300 diseases integrated from databases including dbEST, TiSGeD, HPA, CTD, and Disease Ontology. This online resource allows users to (i) query organ-specific genes/proteins by gene, protein, organ, or disease, (ii) browse organ-specific genes/proteins by human organ system and disease ontology, (iii) explore a histogram of each organ-specific gene/protein, and (iv) identify disease-related genes or disease-related organs.
EGFRindb
Gathers biological and chemical information on epidermal growth factor receptor (EGFR) inhibitors from the literature. EGFRIndb is a database that facilitates better understanding of the molecular space and its associated complexity with reference to EGFR family inhibitors. It provides a resource of almost 4600 small molecules that have shown activity against either of EGFR isoforms (EGFR, ErbB2, ErbB4) or mutants of EGFR-TK domain.
SNP2Structure
Annotates mutated positions both in protein sequences and their associated X-ray and solution nuclear magnetic resonance (NMR) structures. SNP2Structure allows users to inspect protein mutations that may affect the interaction with other macromolecules. It permits exploration of potential structural and functional impact of missense mutations in various human diseases. The database allows users to download the structural models for further structural and functional analysis.
MeioBase
Provides information related to meiosis such as tools for search, comparison and analysis. MeioBase offers access to various kinds of information related to meiosis. It contains a collection of links that give access to many other resources such as the commonly used databases, powerful web servers for molecular and genomic analysis, and experimental protocols for meiosis research.
Carnation DB
Offers a genetic linkage map for carnation. Carnation DB was constructed by employing simple sequence repeat (SSR) markers derived from RNA-seq analysis. The database is dedicated to Dianthus caryophyllus L. It provides information about assembled scaffold sequences, known and novel repetitive sequences, genes for non-coding RNA (tRNA, rRNA, snoRNA and miRNA) and potential protein-encoding genes.
SpliceProt
Provides predicted alternative spliced variants translated in silico and based on experimental human transcriptomic data. SpliceProt applies the ternary matrix methodology to reconstruct the transcripts according to their splicing patterns. It assists researchers to detect splice variants not present in other sequence repositories by facilitating utilization of raw mass spectrometry (MS) proteomics data.
LexEBI / Lexical Entities of Biological Interest
Provides a terminological resource that can serve as a hub for modern language processing techniques and data integration solutions connecting literature with biomedical data. LexEBI is composed of (1) the full scope of biomedical-chemical relevant terms, (2) abbreviations and their long forms from the scientific literature, and (3) frequency information from the scientific literature.
PROTICdb
Allows users to manage laboratory data and publication on the Web with an interface allowing sophisticated queries. PROTICdb is a database that permits annotation of data, and extraction for data mining. It offers a way for researchers to define their own controlled vocabulary and encourages them to use ontology terms defined by the scientific community. This database integrates proteomic data with other types of data and allows building of federative portals.
Ricedb
Performs integrated searches for functional annotations, subcellular location, expression levels, and putative or known regulatory elements, as well as showing orthologues between rice and Arabidopsis. Rice DB can reveal putative function annotations from a variety of sources, expression annotations, predicted subcellular localization, experimentally determined location as well as the phenotypes for proteins with experimentally confirmed subcellular locations, and simply link to the Arabidopsis orthologues(s).
TOBIKOBACHI
Gathers information about Japanese Encyrtid wasps. TOBIKOBACHI is a photograph library based on a personal collection published to help entomologists and biologists as well as taxonomists in getting species information with detailed images. Each entry is composed of 16 items such as scientific names, Japanese name, distribution data, notes or flying season. Images aims to show different parts of the body like the general habitus, thorax, antenna or mandible.
AcEST / Adiantum capillus-veneris EST
Gathers information about over 30 000 expressed sequence tag (EST) clones from the fern Adiantum capillus-veneris.
Taxonomy Icon
Provides a repository of illustrations available for Fungi, Animals, Protists, Plants and Bacteria. Taxonomy Icon includes over 200 images free for use and distribution. The database provides four types of icons: Large, Small, Large with No Background, Small with No Background. Searches can be made by simple or advanced searches.
Invasive Species of Japan
Compiles information about invasive species detected in Japan. Invasive Species of Japan allow searches by taxon among animals and plants and selection among the complete list of all species available in the repository. Besides, the database includes links towards online resources and a way for creating RSS’ alerts about researched species.
JECDB / Japan Existing Chemical Data Base
Gathers reports about toxicity test generated by Japan's existing chemicals safety program. JECDB gives access, for each entry, to a nomenclature of the chemicals accompanied by abstracts and compiled data. Searches can be made by CAS registry number, name or toxicity test. The database also includes a list of chemical substances tested and a list of reports included in the repository.
APASD / Asian-Pacific Alien Species Database
Compiles information about invasive species detected in Asia Pacific countries. APASD is divided by the collected data into eight categories: bacteria, fungi, insect, mammal, nematode, plants, viruses and other animals. Each entry is described with an individual record compiling details such as taxonomic description, images, expansion of distribution area or countermeasure taken.
VegMarks
Compiles information about genetic marker in vegetable crops developed by National Institute of Vegetable and Tea Science (NIVTS). VegMarks gathers data about DNA markers including characteristics such as map position, nucleotide sequence of the clones or PCR primers. Searches can be made by marker or by genotypes thanks to detailed search form. However, some additional data are restricted to registered users only.
AlliumMap
Gathers information about Allium species. AlliumMap includes over 1,700 markers from 10 Allium maps and more than 500 correspondences between markers on different Allium maps. Resources can be browsed through direct links to maps organized by species and publication, or through a CMAP interface. The resource will enable comparative genomics approaches, particularly for basic studies of plant physiology, metabolism and bioprotection in onion and Allium fistulosum.
ICG / Internal Control Genes
Provides access to information about internal control genes for Real-time quantitative (RT-qPCR) normalization. ICG is a wiki-based, publicly editable and open-content resource for community curation of internal control genes across a diversity of species. The database stores experimentally validated internal control genes as well as their associated application scenarios across several species. It allows users to search by gene or species name, provides statistics for species, internal control genes, and experiment conditions and generates a word cloud for visualizing the most prominent terms.
DISNOR
Supports the assembly of disease-related signaling networks to help infer the pathways disrupted in any specific disease. DISNOR is a resource that links disease-associated genes (extracted from the DisGeNET resource) via causal relationships annotated in the SIGNOR database. The database thus connects about 600 gene-products, whose mutations are associated to a specific pathological condition.
ChannelsDB
Provides information about the channels (pores and tunnels) found in entries from the Protein Data Bank (PDB). ChannelsDB is a resource that contains information about the presence and positions of channels in biomacromolecular structures and about local geometrical properties and residues lining the channel and their physicochemical properties. It can be useful for analysis which includes the transport of ligands and other small molecules within biomacromolecular structures.
CR2Cancer
Gathers information about chromatin regulators (CRs) in human cancer. CR2Cancer is a database that allows users to explore the functional, genomic, transcriptomic, proteomic, clinical, biological network and literature-reported information for CRs across multiple cancer types. It contains about 400 CRs annotated with eleven categories of knowledge. CR2Cancer can be useful for investigators in cancer epigenetics research community.
dryAR
Provides a repository for an experiment comprising rainfall-manipulation practiced on Arabidopsis thaliana. dryAR compiles a high-throughput field experiment which has generated an important dataset to study natural selection and adaptation in the context of global climate change at the genetic level.
ScaPD / Scaffold Protein Database
Provides an information’s repository for scaffold proteins and associated signaling pathways. ScaPD contains more than 270 scaffold proteins and over 1100 distinct scaffold-mediated phosphorylation pathways. The database is manually curated from, in part, Google Scholar and PubMed literature and, in other part, from a bioinformatic approach for detecting scaffold proteins. Users can download predicted or experimental datasets or browse a specific search.
ITSoneDB
Informs user about whole eukaryotic domain. ITSoneDB is a database aimed at promoting Internal Transcribed Spacer 1 (ITS1)-based metagenomic surveys. It contains more than one million ITS1 sequences spanning over 134 000 species. Single or multiple entries can be selected for web visualization and/or retrieval through different query options. User can browse this platform by three ways: thanks to a simple search, a tree search, and an advanced search.
EWET-DB / EmsB Website for Echinococcus Typing – DataBase
Records, shares and provides access to data about E. multilocularis, focusing on the EmsB microsatellite. EWET-DB consists in a reference collection dedicated to Echinococcus genetic data. Users can consult isolate data (including EmsB data) and distribution map from the database using different criteria (host, country, province, year of sampling, etc.). The database also allows researchers to perform genetic and spatial analyses on the reference collection and their own data.
NEMiD / North-East India Microbial database
Provides information about microbial diversity in North-East (NE) India. NEMiD aims to answer primary and integrative analysis questions frequently asked by microbiologists and biotechnologists. The database contains more than 200 entries of bacteria, fungi, and actinomycetes along with research articles on database-related data. Users can query different types of information including details of the organism, molecular data and publications. NEMiD can be used to understand the microbial diversity pattern of the megabiodiversity region and to assist in identification of microbes.
PepBase
Gathers information about mass spectrometry (MS)/MS spectra. PepBase is a peptide database that consists in a grouping of experimental data handled by a single analytical platform at the proteomics laboratory of IAB.
Jatropha Genome Database
Gathers information about Jatropha plant. Jatropha Genome Database allows user to find data by two ways: (1) a keyword search mode, and (2) a similarity search mode (where user can specify a type of database, a search program, or a query sequence).
Clover GARDEN / Clover Genome And Resource Database Entry
Supplies data about clover (Genus Trifolium). Clover GARDEN is a resource that focuses on information about genetics and genomics in Trifolium and other legume species. It was designed with more than 450 assembled genome sequences from Illumina and Roche and a high-density single nucleotide polymorphism (SNP) linkage map.
HVDB / Human Variation Database
Stores information about human mutation data. HVDB contains several types of information such as structural variations and repeat variations with statistical genetics analysis results. It supplies different ways of browsing: by disease name, gene name, or chromosome. It also offers overview of single-nucleotide polymorphism (SNP) density or summary of all diseases.
HLA DB / HLA Database
Holds information about human leukocyte antigen (HLA). HLA DB is a repository system containing HLA haplotype data and disease-related information. This resource can be browse by two ways: (1) a sequence search and (2) a HLA search (where user enters information according to disease type, p-value, and more).
CNV association DB / Copy Number Variation association Database
Informs about copy number variation (CNV) association. CNV association DB is an online resource that puts in storage CNV region data, or results of one research laboratory. The database can be browse by informing CNV keyword search, whole genome, or region.
CNV DB / Copy Number Variation Database
Handles copy number variation (CNV) data. CNV DB is a resource that includes information about CNV region data and also results concerning research laboratory. The online platform offers several research modes: (1) CNV keyword search; (2) list of whole genome; (3) region search; and (4) a genome browser.
SNP Control Database
Collects information related to single-nucleotide polymorphism (SNP) genome. SNP Control Database makes available information to assist user in evaluation of appropriate thresholds of quality controls. This resource supplies SNP data to realize case-control study. It stores SNP annotations, allele frequencies and genotype frequencies.
GWAS DB / Genome Wide Association Database
Gives information about genome wide association (GWAS). GWAS DB is an online resource that provides: (1) graphic viewer to search disease related SNP candidates; (2) frequency data such as genotype frequencies and allele frequencies; (3) statistical genetics analysis results such as additive model, recessive model, allelic model, and dominant model.