Citation analyticsNew
Protocol design
Bioinformatics tools
aGEM / anatomic Gene Expresssion Mapping
Conceived to integrate phenotypic information from spatial and temporal distribution of expressed genes in human and mouse.
GCOD / GeneChip Oncology Database
Offers a set of publicly available microarray expression data on Affymetrix genechip arrays related to human cancers. GCOD is composed of normalized and scaled values allowing comparison across studies. It is filtered based on quality control (QC) analysis of the data. This database permits researchers to compare the expression of a single gene across a large number of samples. Its sample annotations are manually curated.
GUDMAP / GenitoUrinary Development Molecular Anatomy Project
An international consortium working to generate gene expression data and transgenic mice. GUDMAP includes data from large-scale in situ hybridisation screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system.
TriplexRNA
A database of cooperating microRNAs and their mutual targets. Using the form on the front page one can be query the database either for human genes or miRNAs to receive information about their possible involvement in RNA triplexes.
HUMSAVAR
An index of human polymorphisms and disease mutations. In release 2015_08 of July 2015, the total number of single amino acid variants annotated in UniProtKB/Swiss-Prot was 71,795. All are listed in the file humsavar.txt. This document also indicates if a single amino acid variant has been reported to be disease-associated (26,874 variants), a neutral polymorphism (38,105), or an unclassified variant (6,816).
MobiDB
Provides a centralized resource for disorder annotation in protein sequences. MobiDB is an online resource that offers the means to obtain disorder annotations for an extensive set of proteins as a centralized and up-to-date source of information on various available disorder flavours. The database features three levels of annotation: manually curated, indirect and predicted. It also includes a consensus annotation for long disordered regions.
AmypDB
An online database dedicated to amyloid precursor families and to their amino acid sequence signatures.
TGDBs / Tumor Gene Family Databases
Provides biomedical researchers with access to information about known tumor genes. TGDBs gathers data about target-genes for cancer-causing mutations, proto-oncogenes and tumor suppressor genes. The database includes (1) the Tumor Gene Database, (2) the Breast Cancer Gene Database, and (3) the Oral Cancer Gene Database.
TSGene
Provides detailed annotations for each tumor suppressor genes (TSGs), such as cancer mutations, gene expressions, methylation sites, transcription factor regulations and protein-protein interactions. The TSGene version 2.0, which has substantial updates of contents (e.g. up-to-date literature and pan-cancer genomic data collection and curation), data types (noncoding RNAs and protein-coding genes) and content accessibility. Specifically, the current TSGene 2.0 contains 1217 human TSGs (1018 protein-coding and 199 non-coding genes) curated from over 9000 articles. Additionally, TSGene 2.0 provides thousands of expression and mutation patterns derived from pan-cancer data of The Cancer Genome Atlas.
PTM-SD / Post Translational Modification Structural Database
Provides access to structurally solved modified residues, which are experimentally annotated as PTMs.
dbGSH
A public resource to allow efficient access to experimentally validated S-glutathionylation sites and comprehensive bioinformatics analyses, including functional annotations, structural characteristics and substrate motifs for S-glutathionylation sites. The database not only provides a benchmark dataset for the development of computational prediction tools and their comparison but also supplies the potential glutathionylated targets for verification and other biological applications.
dbSNO
A database that integrates the experimentally verified cysteine S-Nitrosylation sites from multiple species. Users are allowed to search a group of interested proteins/genes and the system reconstructs the SNO regulatory network based on the information of metabolic pathways and protein-protein interactions.
dbOGAP
A database of O-GlcNAcylated proteins and sites based on experimental data curated from literature as well as from collaborating labs. The resource will facilitate research on O-GlcNAcylation and its proteomic identification.
topPTM
A database that integrates experimentally verified post-translational modifications (PTMs) from available databases and research articles, and annotates the PTM sites on transmembrane proteins with structural topology.
TMPad / TransMembrane Protein Helix-Packing Database
An integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins.
TOPDB / Topology Data Bank of Transmembrane Proteins
Contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins. TOPDB collects details of various experiments that were carried out to learn about the topology of particular transmembrane proteins.
RedoxDB
Provides information about protein oxidative modification verified by experimental studies. For each modified cysteine, the exact position, modification type and flanking sequence are provided. Additional information, including gene name, organism, sequence, literature references and links to UniProt and PDB, is also supplied. The database supports several functions including data search, blast and browsing. RedoxDB not only includes data from case-by-case studies but also integrates high-throughput data from proteomics studies. RedoxDB is useful for both experimental studies and computational analyses of protein oxidative modification.
LNCipedia
Deals with human long non-coding RNA (lncRNA) transcripts and genes. LNCipedia provides information about transcript information and structure, as well as statistics for each record including secondary structure information or microRNA binding sites. Users can query lncRNA sequences and structures according to their criteria of interest and download results in several format, such as GFF and FASTA format.
lncRNome
A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans. lncRNome hosts information on over 17,000 long noncoding RNAs in Human. The resource provides information on the types, chromosomal locations, description on the biological functions and disease associations of long noncoding RNAs.
GeneTests
Offers a medical genetics information resource for physicians, genetic counselors, healthcare providers and researchers. GeneTests promotes the appropriate use of genetic testing and its use in diagnosis, management, genetic counseling, and personal decision-making. It provides current, easy to access information on test availability. The database aims to improve and simplify the users’ searches for tests, clinics, and related information from external links.
TransmiR
Deals with literature-curated transcription factors (TF)-miRNA regulation data about more than 15 organisms. TransmiR is a repository built around three main features: (i) database query, which can be searched by name of either a TF or a mirna , (ii) network visualization, to display data of interest as a network diagram; and (iii) enrichment analysis, allowing the retrieving of overrepresenting TFs.
CSRDB / Cereal small RNAs Database
A bioinformatics resource for cereal crops consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing.
PlantGDB
A genomics database encompassing sequence data for green plants (Viridiplantae).
PlantNATsDB / Plant Natural Antisense Transcripts DataBase
A platform for annotating and discovering NATs by integrating various data sources. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs.
PlantsP
Focuses on plant protein kinases and protein phosphatases.
RNA FRABASE
Provides a resource for the automatic search of user tailored, three dimensional fragments within a set of RNA structures. RNA FRABASE is a web-accessible database with an engine for automatic search of the 3D fragments. It includes a large collection of structural data about RNA molecules, in both their isolated and complexed form, all of which is derived from their PDB deposited atom coordinates.
BPS
A database of RNA base pairs with quantitative information on the spatial arrangements of interacting bases, including higher-order base associations, and the context of these interactions in high-resolution crystal structures.
RNAMDB / RNA Modification Database
Provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. RNAMDB employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry provides the chemical structure, common name and symbol, elemental composition and mass, CA registry numbers and index name, phylogenetic source, type of RNA species in which it is found, and references to the first reported structure determination and synthesis. RNAMDB serves as a primary information portal for researchers across the entire spectrum of RNA-related research.
RNA CoSSMos / RNA Characterization of Secondary Structure Motifs
A freely accessible and searchable online database and website of 3D characteristics of secondary structure motifs.
BGI-RIS / Rice Information System
Provides an integrated resource database for rice data storage, retrieval, visualization and analysis. BGI-RIS provides both an information resource and a comparative analysis workbench for genomic research of rice, other cereal crops and plants. This resource is focused on assembling contigs and anchoring contigs/scaffolds onto the rice chromosomes based on mapped genetic markers and BAC-based physical maps.
MCDRP / Manually Curated Database of Rice Proteins
A literature based manually curated protein centric database of rice proteins. MCDRP provides experimental data embedded in published articles in a computer searchable format. The database has data for over 1800 rice proteins curated from >4000 different experiments of over 400 research articles. It also has protein–protein interaction data for 199 rice proteins as well as DNA–protein interaction data for 51 rice proteins.
OryGenesDB
A search database for rice reverse genetics. OryGenesDB contains flanking sequence tags of various mutagens and functional genomics data, collected from both international insertion collections and the literature. OryGenesDB is also a user-oriented web application that automates and organizes web queries in rice functional genomics. Users can run their queries and store the output and update the results as the source databases are continuously independently updated. OryGenesDB offers a way to accelerate the manual process of integrating and compiling data from heterogeneous sources.
OrysPSSP / Platform for Small Secreted Proteins
A comparative platform for small secreted proteins (SSPs) from rice and other plants. OrysPSSP provides users with several flexible tools and integrates related genome resources to search, validate, filter and compare the data. OrysPSSP serves as a comprehensive resource to explore SSP on the genome scale and across the phylogeny of plant species.
RAP-DB / Rice Annotation Project Database
A comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare.
COMPARTMENTS
An automatically updated web resource to be able to provide up-to-date information on the subcellular localization of proteins from the major eukaryotic model organisms.
DBSubLoc / Database of Protein Subcellular Localization
A database of protein subcellular localization. This database contains proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross referencs to taxonomies and Gene Ontology database.
eSLDB / eukaryotic Subcellular Localization DataBase
A database of protein subcellular localization annotation for eukaryotic organisms.
LOCATE
A curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.
LocDB
An expert curated database that collects experimental annotations for the subcellular localization of proteins in Human (Homo sapiens) and Weed (Arabidopsis thaliana).
CottonGen
Gathers public genomic, genetic and breeding data for cotton. CottonGen is composed of whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. It can be explored through genome pages, search tools and GBrowse, a popular genome browser. This tool permits users to view and compare cotton genetic maps.
GDR / Genome Database for Rosaceae
Provides a curated and integrated repository of Rosaceae genetics, genomics and breeding data and analysis tools. GDR gathers information on quantitative trait loci (QTL), Mendelian trait loci (MTL) or genes and markers for essential agriculture traits from large-scale genotype/phenotype/transcriptome datasets. It includes also data about publications on Rosaceae and several online analysis tools to exploit the collected information.
LIS / Legume Information System
A genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes.
LegumeIP
Hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes. Our recent updates in LegumeIP 2.0 include gene and protein sequences, gene models and annotations, syntenic regions, protein families and phylogenetic trees for six legume species: Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinum (chickpea) and Cajanus cajan (pigeon pea) and two outgroup reference species: Arabidopsis thaliana and Poplar trichocarpa. All expression profiles were manually curated, annotated using free text descriptions, keywords and further hierarchically organized following the Experimental Ontology (EO) and Plant Ontology (PO), allowing users to browse, search and retrieve gene expression profiles for the experiments of their choice using both the EO tree view browser and comprehensive keyword searches. This integrative gene atlas is essential and extremely valuable for the study of gene function and provide valuable large-scale gene expression data to biologists through user-friendly web interfaces.
NRESTdb
Consists of EST sequences, BLASTX search results against the non-redundant protein database (NR), Pfam and InterPro, annotations based on KOG, Inparanoid and GO classifications, enhanced datasets related to rubber research topics of interest.
SoyXpress
A database (MySQL) designed for exploring the soybean transcriptome. SoyXpress is designed for the purpose of exploring potential transcriptome differences in different plant genotypes, including genetically modified crops. Soybean EST sequences, microarray and pathway data as well as searchable and browsable gene ontology are integrated and presented.
SGMD / Soybean Genome and Microarray Database
Attempts to provide an integrated view of the interaction of soybean with the soybean cyst nematode and contains genomic, EST and microarray data with embedded analytical tools.
Shanghai RAPESEED Database
Provides the solid platform for functional genomics studies of oilseed crops with the emphasis on seed development and fatty acid metabolism. The RAPESEED includes the resource of 8462 unique ESTs, of which 3526 clones are with full length cDNA; the expression profiles of 8095 genes and the Serial Analysis of Gene Expression (SAGE, 23,895 unique tags) and tag-to-gene data during seed development. In addition, a total of approximately 14,700 M3 mutant populations were generated by ethylmethanesulfonate (EMS) mutagenesis and related seed quality information was determined using the Foss NIR System.
StaphyloBase
Developed with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations.
AureusDB
A S. aureus database, provides access to the genome sequences of various S. aureus strains and related species.
VFDB / Virulence Factor DataBase
Provides up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens. VFDB allows usres to investigate the diversity of bacterial genomes in terms of virulence by highlighting common and species- or strain-specific VFs. It provides an extended sequence similarity search among the full dataset allowing the discovery of potentially overlooked VFs. This platform can be used to construct conserved domain profiles for each component of all VFs.
TIGR Maize Database
A repository of publicly available maize genomic sequences.
ZMP / Zebrafish Mutation Project
Aims to create a knockout allele in every protein coding gene in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing. Each allele created is analysed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype.
Zebrafish TILLING Project
The goal of this project is to use TILLING to generate and distribute loss-of-function mutations in genes of interest to the zebrafish community. The zebrafish TILLING project is a joint effort of the Moens lab at the Fred Hutchinson Cancer Research Center and the Solnica-Krezel lab at Washington University School of Medicine in St. Louis.
BCL2DB / BCL-2 Database
A collection of sequence, structural and functional information about BCL-2 homologous and BH3-containing proteins, which are among the most studied in cell biology. The Web interface allows for easy browsing of the site and fast access to data, as well as sequence analysis with generic and specific tools. BCL2DB provides a helpful and powerful tool to both 'BCL-2-ologists' and researchers working in the various fields of physiopathology.
CGED / Cancer Gene Expression Database
A database of gene expression profile and accompanying clinical information.
CircaDB / Circadian Expression Profiles Data Base
A database of circadian transcriptional profiles from time course expression experiments from mice and humans. Each transcript's expression was evaluated by three separate algorithms, JTK_Cycle, Lomb Scargle and DeLichtenberg. Users can query the gene annotations using simple and powerful full text search terms, restrict results to specific data sets and provide probability thresholds for each algorithm.
COLOMBOS
A collection of expression data from both microarray and RNA-Seq experiments for several prokaryotic species, taken from publicly available database such as the Gene Expression Omnibus (GEO) and ArrayExpress. Its uniqueness resides in the ability to cope with data heterogeneity and directly integrate data coming from different platforms and technologies.
dbERGE / Database of Experimental Results on Gene Expression
Houses both detailed experimental data and summary of experimental results and provides a convenient query interface and display options for quick retrieval of interesting data. Its applications include archiving data in a queriable manner, finding all experimental results in a targeted genomic locus and assessing biological meaning from high-throughput data.
UMD TP53 database
A reference for all scientists working on p53, including information on p53 structure and function, the description of all p53 monoclonal antibodies and the phylogenetic analysis of p53. More than 50% of human tumors carry TP53 gene mutations and in consequence more than 45,000 somatic and germline mutations have been gathered in the UMD TP53 database. Analyses of these mutations have been invaluable for bettering our knowledge on the structure-function relationships within the TP53 protein and the high degree of heterogeneity of the various TP53 mutants in human cancer.
ALE-HSA21 / AnaLysis of Expression of HSA21
An integrated and a user-friendly relational database, which provides detailed information about various aspects of genes mapping on chromosome 21, such as gene structure, expression, nucleotide variations and association to diseases.
OpenfluDB / OpenFlu database
An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB.
IRD / Influenza Research Database
A comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data. IRD comprises (i) a comprehensive collection of influenza virus related data integrated from public archives, data submitters and IRD in-house curation and annotation pipelines, with data types covering sequences and sequence annotations from GenBank and UniProt, (ii) a growing suite of analytical and visualization tools customized for influenza virus data analysis and (iii) personal workbench spaces for data storage and sharing.
Canto
A web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase.
3DSwap
A comprehensive collection of protein structures that are reported to be involved in 3-Dimensional Domain Swapping.
CDD / Conserved Domain Database
Provides a public repository for annotation of proteins. CDD includes more than 56 000 records from all sources database dispatched into 5 600 multi-model superfamilies. The database incorporates biomolecular sequences accompanied by the location of evolutionarily conserved protein domain footprints and links to functional sites related to them. Searches can be made by protein or nucleotide query, accession, GI number, or with a sequence in FASTA format.
DomIns
Provides information on domain insertions in known protein structures. DomIns is a web resource using the Structural Classification of Proteins (SCOP) protein domain definitions to identify insertions. It allows user to search by (i) Protein Data Bank (PDB) or SCOP identifier, (ii) keywords, (iii) browsing all insertions, (iv) by insertion type or (v) by SCOP class combination. The database can be used to undertake studies on the effect of domain insertions on protein folding and to expand the repertoire of multifunctional hybrid proteins.
BloodSpot
Provides an expression plot of genes in healthy and cancerous hematopoietic cells at specific differentiation stages. BloodSpot allows hypothesis testing and generation, via gene-centric lookup of mRNA expression throughout the course of hematopoiesis. It contains data about the definition and inclusion-criteria for each cell type, avoiding researchers to find original papers. This database is useful in the fields of leukemia, hematopoiesis, cellular development, or stem cells.
Hembase
Assists with the examination of the human erythroid transcriptome. Hembase is an integrated browser and genome portal that provides hematologists with a genome-based approach toward the study of erythroid biology. It contains more of 15 000 entries from erythroblast expressed sequenced tags (ESTs) and almost 380 referenced genes relevant for erythropoiesis. This resource is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry.
HemoPDB / Hematopoiesis Promoter Database
A comprehensive resource focused on transcriptional regulation during hematopoietic development and associated aberrances that result in malignancy.
HPMR / Human Plasma Membrane Receptome
Receptome genes have been matched with their ligands for surveying DNA microarray datasets.
HuGEIndex / Human Gene Expression Index
Aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues.
ITTACA / Integrated Tumor Transcriptome Array and Clinical data Analysis
A public database that gathers published clinical and transcriptomic datasets for bladder and breast carcinomas, and uveal melanoma. These data are made available on the Internet for users to reanalyze and study. Several analysis tools allow users to define new patient groups, search for differentially expressed genes, assess differential gene expression, study patient survival time and perform some statistical analyses of gene expression.
Animal QTLdb / Animal Quantitative Trait Loci database
Provides quantitative trait loci (QTL) data for cattle, chicken and pigs. AnimalQTLdb enables comparison of QTL results within species and across experiments. It serves as a bridge between genotypes (genes) and phenotypes (traits), which will inevitably necessitate inclusion of single nucleotide polymorphism (SNP)/genome-wide association study (GWAS) data. The database contains about 5900 cattle, 3400 chickens, 7400 pigs, 750 sheep and 90 rainbow trout data points.
ARKdb
Provides genome mapping data from farmed species and other animals. ARKdb contains information details of loci, maps, experimental methods and the source references of twelve species: cat, chicken, cow, deer, duck, horse, pig, quail, salmon, sea bass, sheep and turkey. It attempts to provide the same functionality as the Mouse genome Database and the Genome Database for their respective animal species.
BGD / Bovine Genome Database
Strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies.
cBARBEL / catfish Breeder And Researcher Bioinformatics Entry Location
An online open-access database for genome biology of ictalurid catfish (Ictalurus spp.).
EMMA / European Mouse Mutant Archive
A leading international network infrastructure for archiving and worldwide provision of mouse mutant strains. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server.
euGenes
A genome information system and database that provides a common summary of eukaryote genes and genomes.
EVOG / Evolution Visualizer for Overlapping Genes
An integrated database for overlapping genes that includes bioinformatics analysis data. EvOG supports all overlapping genes that are common in a subset of Human, Chimpanzee, Orangutan, Marmoset, Rhesus, Cow, Dog, Mouse, Rat, Chicken, Xenopus and Zebrafish. In addition, it provides a manually curated database that displays the evolutionary features of overlapping genes. The EvOG database is very effective and easy to use for the comparative analysis and investigation of evolutionary processes of overlapping genes. Furthermore, the EvOG database supports a visualization interface that shows the comparative configuration of overlapping genes across multiple species along the whole chromosome scale. The database is constantly being supplemented with new genome data from a range of other available sources.
Gallus GBrowse
Provides online access to genomic and other information about the chicken, Gallus gallus.
IMPC / International Mouse Phenotyping Consortium
Provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and standardized protocols for the experimentation, collection and dissemination of data. Dedicated 'data wranglers' work with each phenotyping center to collate data and perform quality control of data. An automated statistical analysis pipeline has been developed to identify knockout strains with a significant change in the phenotype parameters. Annotation with biomedical ontologies allows biologists and clinicians to easily find mouse strains with phenotypic traits relevant to their research. Data integration with other resources will provide insights into mammalian gene function and human disease.
MfunGD
Provides a resource for annotated mouse proteins and their occurrence in protein networks.
CED / Conformational Epitope Database
A special database of well-defined conformational epitopes. CED provides a collection of conformational epitopes and related information including the residue make up and location of the epitope, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope. All entries in this database are manually curated from articles published in peer review journals.
EPIMHC
A relational database of MHC-binding peptides and T cell epitopes that are observed in real proteins. Currently, the database contains 4867 distinct peptide sequences from various sources, including 84 tumor-associated antigens. The EPIMHC database is accessible through a web server that has been designed to facilitate research in computational vaccinology. Importantly, peptides resulting from a query can be selected to derive specific motif-matrices. Subsequently, these motif-matrices can be used in combination with a dynamic algorithm for predicting MHC-binding peptides from user-provided protein queries.
ImmunomeBase
A database for metazoan immunity genes and orthologs. All the immunity genes and their evidence of immune function, orthologs and ortholog groups have been combined into an open access database.
GOBASE
A taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.
Organelle DB
Provides an information resource cataloging eukaryotic proteins that are known components of an organelle or major protein complex. Organelle DB is a web-accessible relational database that presents a list of proteins organized essentially by subcellular localization and/or by organism. Users can search for proteins localized to a given organelle, subcellular structure or protein complex. The scientific visualization application Organelle View allows users to dynamically generate a visual interpretation of data from Organelle DB.
HMPDb / Human Mitochondrial Protein Database
Provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function.
HmtDB / Human Mitochondrial Database
Supports population genetics and mitochondrial disease studies. HmtDB hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar/MitVarProt programs, based on site-specific nucleotide and aminoacid variability calculations. The annotations are manually curated thus adding value to the quality of the information provided to the end-user. Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user. Haplogroup definition is based on the Phylotree system. End-users accessing HmtDB are hence allowed to: (i) browse the database through a multi-criterion query system; (ii) analyse their own human mitochondrial sequences via the classify tool or by downloading the mt-classifier tool; (iii) download multi-alignments with reference genomes as well as variability data.
MitoData
A unique multi-national database holding clinical, biochemical and molecular genetic data on human mitochondrial diseases.
MitoGenesisDB
Focuses on the dynamic of mitochondrial protein formation through global mRNA analyses.
MitoMiner
Deals with mitochondrial proteomics. MitoMiner is a gene-centric resource that integrates different types of subcellular localisation evidence with protein information from public resources. Searches can be made by text searches, predefined or customized queries by the use of the QueryBuilder module. It allows users to investigate mitochondrial proteins, with application in mitochondrial research, such as the ability of prioritize candidate mitochondrial disease genes.
MitoRes
A comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. MitoRes has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions.
MitoZoa
Provides manually curated data on gene annotation, gene order, gene content and non-coding regions (NCR) of complete and nearly-complete mitochondrial genomes (mtDNA). MitoZoa is an online database collecting sequences from all metazoan species, and systematically identifies and resolves gene misannotations. Moreover, this It also offers several additional types of information and search options.
MPIMP db / Mitochondrial Protein Import Machinery of Plants database
An Internet-accessible database containing detailed information on the protein import apparatus of plant mitochondria.
OGRe / Organellar Genome Retrieval
A searchable relational database which currently contains the complete mitochondrial genome sequences of 1244 metazoan organisms.
YDPM database / Yeast Deletion Project and Proteomics of Mitochondria Database
The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell.
COMPEL
A database on composite regulatory elements, the basic structures of combinatorial regulation. Composite regulatory elements contain two closely situated binding sites for distinct transcription factors and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor-DNA and factor-factor interactions contribute to the function of composite elements (CEs). Information about the structure of known CEs and specific gene regulation achieved through such CEs appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well.
CSNDB / Cell-signaling networks database
Provides all the biological properties of cellular signal transduction, including biological reactions that transfer cellular signals and molecular attributes characterized by sequences, structures, and functions.
DopaNet
Serves for the study of all the aspects of neurotransmission in the mesotelencephalic dopamine system. DopaNet provides molecular pages composed of structured descriptions of quantitative parameters related to a specific molecular complex involved in neuronal signal processing. It contains a specific ontology code, annotated (method of acquisition, species, etc.) and linked to a relevant bibliography.