Tag: mapping

Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

The Genome-Wide Association Studies (GWAS) Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignm ...

The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually an ...

BRCA Share is a novel gene datashare initiative that provides scientists and commercial laboratory organizations around the world with open access to BRCA Share (formerly UMD-BRCA1) contains BRCA1 and BRCA2 genetic data. The program’s goal is to acce ...

The Stanford HIV Drug Resistance Database (HIVDB) is an essential resource for public health officials monitoring ADR and TDR, for scientists developing new ARV drugs, and for HIV care providers managing patients with HIVDR.

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

T-DNA insertions in Arabidopsis and their flanking sequence tags.

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

CottonGen is a cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. CottonGen supercedes Cotto ...

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitati ...

Curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

dbSTS is an NCBI resource that contains sequence data for short genomic landmark sequences or Sequence Tagged Sites.

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

The international glycan structure repository for glycans published in the literature. Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered and have an accession number assigned as ...

OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ort ...

The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research ...

The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.

microRNA-mRNA interaction maps

REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence ...

GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.

Tool for visualising the syntenic context of any gene from several yeast genomes.

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that ...

The objective of this project is to generate the most comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications.

A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database ...

This database summarizes our knowledge of replication origins in the budding yeast Saccharomyces cerevisiae. Each proposed origin site has been assigned a Status (Confirmed, Likely, or Dubious) expressing the confidence that the site genuinely corres ...

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...

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

GWAS Central stores genome-wide association study data. The database content comprises direct submissions received from GWAS authors and consortia in addition to actively gathered data sets from various public sources. GWAS data are discoverable from ...

Autism genetics KnowledgeBase, an evidence-based knowledgebase of autism genetics.

Genome database of the beetle Tribolium castaneum

Type II Toxin-Antitoxin loci in bacteria and archaea

U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.

ReMap is an integrative analysis of transcription factor ChIP-seq experiments publicly available, merged with the Encode dataset. The resource is an extensive regulatory catalogue of transcription factor binding sites from transcription factors (TFs) ...

Gene Signature DataBase

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 genomes.

SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...

DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. The database includes published and unpublished low and high throughput data sets, ...

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.

Deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, C. intestinalis, D. melanogaster, C. elegans and A. thaliana. It facilitates the comprehensive annotation and discovery o ...

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarra ...

EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB ...

NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.

The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes.

The GrainGenes website hosts a wealth of information for researchers working on Triticeae species, oat and their wild relatives. The website hosts a database encompassing information such as genetic maps, genes, alleles, genetic markers, phenotypic d ...

Polbase is an open and searchable database providing information from published and unpublished sources on the biochemical, genetic, and structural information of DNA polymerases.

Data Repository for Yeast Genetic Interaction Networks

PGG.SNV is database for understanding the evolutionary and medical implications of human single nucleotide variation (SNV) on a population level. It documents more than 300,000 genomes and 10 billion allele frequencies records for diverse human ethni ...

WebGesTer Database (DB) is the largest compilation of intrinsic terminators of transcription. It comprises of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. The database is the storehouse for algorithm ...

The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context.

euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, ...

Human Histone Modification Database

Essential gene profiles in human cancer cell lines

>>>!!! <<< The Epigenomics database was retired on June 1, 2016. All epigenomics data are available in our GEO resource https://www.ncbi.nlm.nih.gov/geo >>> !!! <<< The Epigenomics database provides genomics maps of stable and reprogrammable nucl ...

Biosynthetic gene cluster families

Kazusa Plant Pathway Viewer

Domain interaction map: experimental and predicted protein domain interactions

AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. Proteins are frequently associated with other molecules to perform their functions. Experimental structures determined in the bound state are named holo s ...

SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biologica ...

The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one ...

GWAS prioritization tool

Mouse Indel Polymorphism Database

General practice database for research.

PmiREN is a comprehensive encyclopedia of plant miRNAs.

An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Table of Multiplexed Assay of Variant Effect (MAVE) studies. MaveDB - A repository for MAVE assay datasets. To cite this document, please use the c ...

ClinEpiDB is an open-access online resource for clinical and epidemiologic studies. The website allows users to visualize and subset data directly in the ClinEpiDB browser and explore potential associations. Supporting study documentation aids contex ...

Wiki on all aspects of next-generation genomics

A comprehensive resource for the genes retained from whole genome duplication in vertebrates. The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison. A Repository of Genes Retained from Whole Genome Duplications in the Vert ...

A database for disease/trait causal variants identified using summary statistics of genome-wide association studies. A GWAS fine-mapping pipeline used in CAUSALdb. CAUSALdb integrates large numbers of GWAS summary statistics and identifies credible ...

System for collecting, preserving and providing bioresources for use as experimental materials for life science research.

Database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB) ...

Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide ...

An integrated omics knowledgebase for molecular breeding in rice. Rice Phenotype Search and Summary. Rice Genotype Search and Summary. Molecular Breeding Knowledge Database. Created with the Personal Edition of HelpNDoc: News and information abou ...

Online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with ...

A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies. VariCarta is a curated, web-based database housing ASD-linked genes created from the meta-analysis of -omic sequencing literature. VariCar ...

GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoconjugate data in RDF.

Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. The first Korean Reference Genome. KOREF_S means KOREF_Single.

Base de Datos para la Investigación Farmacoepidemiológica en Atención Primaria (BIFAP) is a population based database administered by the AEMPS (Spanish Agency for Medicines) of longitudinal electronic medical records (EMR) of patients attended in pr ...

A web application for the generation, storage, and presentation of genome-wide analyses of mutually exclusive exonomes.

Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources ...

3DSNP is a database for comprehensively annotating the regulatory function of human noncoding SNPs by exploring their 3D interactions with genes and genetically associated SNPs mediated by chromatin loops. 3DSNP integrates Hi-C data together with a v ...

A comprehensive, annotated database of microsatellites. Multiple Loci VNTR Analysis databases and software. Multi Locus VNTR Analysis (MLVA) databases and software. MICAS 3.0, Microsatellite Analysis Server is the online repository of All Bacteria ...

WheatQTLdb is a manually curated QTL database for wheat that includes information about QTL identified through interval mapping and MTA identified using GWAS.

A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases. Jun 1, 2018: Startup of the ncRNAVar project.... Sep 10, 2019: The variant mapping was developed...

An online database towards comprehensive essential gene annotation for prokaryotes.

Database and analysis platform for pathogenic E. coli transcriptional gene regulatory networks. The database contains the known regulatory network of E. coli K-12 extracted from RegulonDB. In addition, it provides inter-species transferred gene regul ...

circ2GO is a comprehensive database compiling and analyzing circular RNAs found in lung cancer cell lines providing the data in tables as well as visualizing it in transcript maps and in heatmaps. Importantly, we also provide easy-to-use online tools ...

KAIKObase is a silkworm genome database.

MSRdb (Mycobacterial Systems Resource) is a mycobacterial systems resource for the research community. The Mycobacterial Systems Resource (MSR) is a comprehensive, integrated biological and bioinformatic resource for the research community. The MSR u ...

A database of Plant Chloroplast Inverted Repeats. Plant Chloroplast Inverted Repeats. Welcome to PCIR! Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables det ...

A major update of the ruminant functional and evolutionary genomics database.

Integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding.

An informational platform for genome biology of grass carp. Grass carp (Ctenopharyngodon idellus) is a herbivorous, freshwater fish species of the family Cyprinidae, and the only species of the genus Ctenopharyngodon.

Integrative database and analysis platform that relates microbiome and phenotypic data. MANTA (Microbiota And pheNotype correlaTion Analysis platform) is an integrative database and analysis platform that relates microbiome and phenotypic data. MANT ...

VannoPortal is a variant annotation database that comprehensively collects and integrates genome-wide variant annotations and prediction scores from various biological domains, including allele frequency, linkage disequilibrium, evolutionary signatur ...

The webTWAS integrates large number of GWAS summary level data for disease, and this number will be constantly increasing according to our timely curation. The webTWAS calculates the causal genes using single tissue expression imputation (MetaXcan an ...

ForageGrassBase is molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.).

AddictGene is an integrated knowledge base for differentially expressed genes associated with psychostimulants,

User-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.

EpiMetal is an open-source graphical web browser tool for easy statistical analyses in epidemiology and metabolomics.

Tools for Influenza Activity and Surveillance. U.S. Influenza Surveillance System. Overview of Influenza Surveillance in the United States - CDC. Centers for Disease Control and Prevention. CDC twenty four seven. Saving Lives, Protecting People. ...

Exploration and analysis of R-loop mapping data with RLBase.

Publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis.

A secondary database derived from primary data in NCBI's short read archive. Database for corrected read counts and genome mapping on NCBI's transcriptomics archives.

The Actinobacteriophage Database.

Database of human genotype-phenotype associations.

PaIntDB (Pseudomonas aeruginosa Interactions Database) is a tool for network-based omics integration and visualization using protein–protein interactions in Pseudomonas aeruginosa. PaIntDB contains more than 150K protein-protein (PPI) and protein-met ...

A comprehensive resource for kiwifruit genomics.

A Grameneae Genome Alignment Database of Homologous Genes Hierarchically Related to Evolutionary Events.

A comprehensive genome platform for Brassicaceae plants.

Database and Tool for Metataxonomics with Long-Read Sequence.

A curated and comprehensive resource of plant cell markers.

An integrative database for traditional Chinese medicine plant genomes.

Advanced Functions Embedded in the Second Version of Database, Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2.

dbCNS is a database for conserved noncoding sequences.

A Database and User Interface for scRNA-seq Marker Genes.

DupScan is a database for visualizing and predicting vertebrate synteny and genome duplication.

A collective database of helmeted guinea fowl genomics. Helmeted guinea fowl (HGF; Numida meleagris) is vigorous, hardy, and mostly disease-free game birds. The rearing of HGF is a potential alternative poultry system. Because of the characteristics ...

GGVD is a goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions.

Rhododendron Plant Genome Database (RPGD) is a comprehensive online omics database for Rhododendron.

MetAMDB is a software/database for the analysis of metabolic models and specifically the work with atom mappings.

MtExpress is a comprehensive and curated RNAseq-based gene expression atlas for the model legume medicago truncatula.

An integrated Web-database for bovine sequencing variations and selective signatures.

FishmiRNA is an evolutionarily-supported, manually-curated, genome duplication-aware database for the annotation of ray-finned fish miRNA genes, their mature products and their expression profiles.

The MRC IEU OpenGWAS data infrastructure. The OpenGWAS database is constantly growing, but there may be studies that users have generated or need to include in their analyses that have not yet been incorporated.

Black Pepper Drought Transcriptome Database (BPDRTDb) catalogues all the genomic information like differential expressed genes, microsatellites, variants, transcriptional factors, pathways, domain and families of assembled transcriptome associated wi ...

proMGE is a resource for the retrieval of 6 Mobile Genetic Element (MGE) categories in 76K genomes (totalling to 2.4 million prokaryotic MGEs) and classification of new ones in user provided protein sequences from genomes and genomic fragments.

A Repository of Experimentally Characterized O-Glycoproteins to Facilitate Studies on O-Glycosylation. Numerous studies on cancer, biopharmaceuticals, and clinical trials have necessitated comprehensive and precise analysis of protein O-glycosylation ...

A database of monosaccharide biosynthesis pathways. Monosaccharide Biosynthesis Pathways Database. Pathways for monosaccharide biosynthesis. Welcome to MonoPathDB, a database of biosynthesis pathways and enzymes for monosaccharides.

CarrotOmics is an integrated web-based relational database, developed to house and integrate genomic, genetic and breeding data for carrot and related species. CarrotOmics includes genome assemblies, annotated transcripts, traits, maps, and markers b ...

The Bibliome Variant Database is a collection of variants mined from open-access primary literature. All variants included in the database have been mapped to the human genome and are presented in a manner ordered by genomic location. The goal of thi ...

ATAV is a comprehensive platform for population-scale genomic analyses. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and single ...

NAGRP Blast Center aggregates various sequence databases and makes them accessible via its website.

A comprehensive genetic resource of nicotine and smoking. Genetic resources of nicotine and smoking. Genetic Resources Of Nicotine and Smoking (GRONS) is a database devoted to provide a comprehensive and systematic collection of cross-platform gene ...

A cross-sectional analysis of the emergency events database from a pediatric perspective. The international disasters database. Disaster group: Two main groups of disasters are distinguished in EM-DAT: natural disasters and technological disasters. ...

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Plasmodium falciparum Community Project. Dried blood spot collection. Photo credit: Will Hamilton. HiSeq machines at the Wellcome Trust Sanger Institute. Photo c ...