Tag: rna

Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the ...

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synth ...

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 ...

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More in ...

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submissi ...

The aim of MIQE is to provide authors, reviewers and editors with specifications for the minimum information that must be reported for a qPCR experiment in order to ensure its relevance, accuracy, correct interpretation and repeatability.

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic ...

MIAME is intended to specify all the information necessary for an unambiguous interpretation of a microarray experiment, and potentially to reproduce it. MIAME defines the content but not the format for this information.

A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.

The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and expe ...

The Cancer Genome Atlas (TCGA) is a comprehensive, collaborative effort led by the National Institutes of Health (NIH) to map the genomic changes associated with specific types of tumors to improve the prevention, diagnosis and treatment of cancer. I ...

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...

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 ...

The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. It is a founding member of the worldwide Protein Data Bank which collects, organises a ...

SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO i ...

Database of RNA interactions in post-transcriptional regulation.

The Ensembl genome annotation system, developed jointly by EMBL-EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented b ...

NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs), including long noncoding (lnc) RNAs. Information contained within the database includes human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationshi ...

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely av ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactio ...

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes ...

The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements ...

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

DRSC Functional Genomics Resources (DRSC-FGR) began as the Drosophila RNAi Screening Center (DRSC), founded by Prof. Norbert Perrimon in 2003, and the Transgenic RNAi Project (TRiP), founded by Prof. Perrimon in 2008. DRSC-FGR has been previously kno ...

GenePattern GeneSet Table Format is an analytical tool and file format for the analysis of gene expression and network analysis provided by GenePattern.

Ensembl Metazoa provides access to genomes of metazoans of interest in disease, environmental sciences, agriculture and economic concern. Extensive coverage exists of diptera, nematodes, lepidoptera and hymenoptera.

Ensembl Protists stores protist genomes of interest, covering those involved in disease and of scientific interest. This includes genomes such as Plasmodium falciparum, Dictyostelium discoideum, Phytophthora infestans and Leishmania major. A majority ...

The Nucleic Acids Database contains information about experimentally-determined nucleic acids and complex assemblies. NDB can be used to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and ...

A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequen ...

The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is e ...

MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that ...

The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of Hepatitis C Virus.

Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of ...

Ensembl Bacteria is a browser for bacterial and archaeal genomes. These are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Databas ...

Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides informati ...

RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In t ...

MycoCosm provides data access, visualization, and analysis tools for comparative genomics of fungi. MycoCosm enables users to navigate across sequenced fungal genomes, and to conduct comparative and genome-centric analyses of fungi and community anno ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing ...

NCBI Viral Genomes Resource is a collection of virus genomic sequences that provides curated sequence data, related information and tools. It includes all complete viral genome sequences deposited in the International Nucleotide Sequence Database Col ...

MISFISHIE is the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments. This specification details the minimum information that should be provided when publishing, making public, or exchanging results from v ...

The BBMRI-ERIC Directory is a tool to share aggregate information about biobanks across Europe. The Directory welcomes new biobanks to join and publish information about themselves, including their contact information in the directory. The BBMRI-ERIC ...

Ensembl Plants holds the genomes of plants of significant interest. These range from those of agricultural importance, those which support primary research and of environmental interest. Ensembl Plants datasets are constructed in a direct collaborati ...

Long Non-Coding RNA Database

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

Predicted structures of internal transcribed spacer 2 (ITS2)

MIAME/Plant is a standard describing which biological details should be captured for describing microarray experiments involving plants. Detailed information is required about biological aspects such as growth conditions, harvesting time or harvested ...

FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes compara ...

The RNA Modification Database contains information pertaining to naturally occurring RNA modifications. The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry pro ...

RNAO is a controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from pri ...

FuzDB compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database ha ...

Nearest Neighbor parameters for predicting RNA folding

Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, di ...

The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) was created to make the raw data of protein crystallography more widely available. The IRRMC identifies, catalogs and provides metadata related to datasets that cou ...

The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation ind ...

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR ...

HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.

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 ...

MIAME defines a conceptual structure for defining the core information that is common to most microarray experiments. MIAME/Env is an extension of these guidelines to cover environmental genomics.

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...

MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Tricho ...

The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that contain secondary structure motifs such as mismatches, (a)symmetric interna ...

The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of informa ...

PseudoBase is a collection of RNA pseudoknots that have been made available for retrieval to the scientific community.

Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each.

GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public ...

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 ...

BioXpress is a curated gene expression and disease association database where the expression levels are mapped to genes.

RNAML syntax was designed to facilitate the interoperation of multiple RNA informatics programs and to exchange basic RNA molecular information.

The bracket notation for RNA secondary structures Pseudo-knot free secondary structures can be represented in the space-efficient bracket notation, which is used throughout the Vienna RNA package.

Database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.

ATCC authenticates microorganisms and cell lines and manages logistics of long-term preservation and distribution of cultures for the scientific community. ATCC supports the cultures it acquires and authenticates with expert technical support, intell ...

BSRD is a resource for bacterial sRNA sequences with extensive annotation and expression profiles. BSRD provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. There is also a novel RNA-Seq analysis pl ...

MINSEQE describes the Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guideline ...

The Mammalian Transcriptomic Database (MTD) was created to store information on mammalian transcriptomes. The MTD allows browsing of genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exo ...

Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utiliz ...

The RDML file format is developed by the RDML consortium (http://www.rdml.org) and can be used free of charge. The RDML file format was created to encourage the exchange, publication, revision and re-analysis of raw qPCR data. The core of an RDML fil ...

RNAiDB provides access to results from RNAi interference studies in C. elegans , including images, movies, phenotypes, and graphical maps.

HuSiDa is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup ...

CDISC Glossary seeks to harmonize definitions (including acronyms, abbreviations, and initials) used in the various standards initiatives undertaken by CDISC in clinical research. Glossary also serves the community of clinical researchers by selectin ...

Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning | Core code for the DeepHF prediction tool | SpCas9 & Base Editor Efficiency Prediction | This tool provides guide designs for Wild-type SpCas9, two highly specifi ...

The noncoding RNAs database is a colection of currently available sequence data on RNAs, which do not have protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous ...

The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch. Linked to these sequences is information including siRNA thermodynamic prope ...

EuRBPDB is a comprehensive and user-friendly database for classifying and annotating eukaryotic RNA binding proteins (RBPs) drawn from various public databases. Over 100 eukaryotic species such as human, mouse, fly, worm and yeast are included. EuRBP ...

rPredictorDB is a predictive database of secondary structures of individual RNAs and their formatted plots.

GenomeTraFaC is a database of conserved regulatory elements obtained by systematically analyzing the orthologous set of human and mouse genes. It mainly focuses on all of the high-quality mRNA entries of mouse and human genes in the Reference Sequenc ...

A database of proteins undergoing liquid-liquid phase separation in vitro. LLPSDB contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments.

siRecords is a collection of a diverse range of mammalian RNAi experiments . After choosing a gene, researchers can find all siRNA records targeting the gene, design a new siRNA targeting it, or submit siRNAs that have been tested. The resource also ...

Integrates information on RNA helicases. The database allows retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Sacc ...

Protein–RNA interaction predictions for model organisms with supporting experimental data, enabling a global view of the protein–RNA interactome. RNAct currently covers the human, mouse and yeast genomes and contains a total of 5.87 billion pairwise ...

DNAzymes i.e. DNA molecules with catalytic activity

The Pig Genomic Informatics System (PigGIS) presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed ...

A CT (Connectivity Table) file contains secondary structure information for a RNA sequence.

GenBank Sequence Format (GenBank Flat File Format) consists of an annotation section and a sequence section. The start of the annotation section is marked by a line beginning with the word "LOCUS". The start of sequence section is marked by a line be ...

Database of single-cell expression map across various human cancers.

RNAPhaSep is a novel database that collects phase separation related RNAs manually curated from publication and public databases. Various properties of RNAs together with the corresponding phase separation conditions validated by experiments were col ...

ViroidDB is the most comprehensive collection of viroid, satellite RNA, retrozyme, and deltavirus genome sequences available on the internet.

An intuitive database of RNA pocket topology information with RNA-ligand data resources.

A database of genus characteristics of proteins and RNA. A database of genus characteristics. The Genus database collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given c ...

Sequence composition dynamics of genes and genomes.

A database for single-cell screening of virus target cells in the animal kingdom.

Database for binding affinities of protein-nucleic acid complexes and their mutants.

Thousands of circular RNAs (circRNAs) have recently been shown to be expressed in eukaryotic cells [Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013]. Here you can explore public circRNA datasets and download the custom ...

PrimateDatabase.com, a publicly available web-accessible archive of intracellular patch clamp recordings and highly detailed three-dimensional digital reconstructions of neuronal morphology. PrimateDatabase.com is unique because it is currently the l ...

Gene annotation portal and a resource on gene and protein function

Genomics of fungal, oomycete and bacterial phytopathogens

<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGen ...

The TBestDB (a Taxonomically Broad EST database) database contains ~370,000 clustered EST sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, conse ...

Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world. This year's update for EMBL-EBI focuses on data exchanges among ...

Collection of samples and data across the following diseases: Sjogren's syndrome (disorder) Peripheral blood samples (DNA, RNA, serum, PBMC) from patients with primary Sjogren's syndrome, with detailed contemporaneous clinical data at the time of sam ...

Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.

A repository of cleaned PDB-derived RNA 3D structures.

RNA aptamer 3D-structural modeling database.

A database of RNA multiloops.

CoDNaS-RNA is a database of the Conformational Diversity in the Native State of RNA molecules. Each entry in CoDNaS-RNA is a redundant collection of known structures of the same RNA molecule, which can be considered as alternative instances of the RN ...

Database of cooperating miRNAs and their mutual targets which enables researchers explore novel patterns in gene regulation.

The RNA G-quadruplex and RG4-binding proteins database.

Comprehensive and non-redundant benchmark for RNA–RNA docking and scoring.

rPanglaoDB is an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. A meta-analysis database for single cell RNA sequencing data. Search across datasets, studies, download data, and perform advanced visualiz ...

A repository for DNA and RNA nanostructures.

The BpForms Grammar extends the IUPAC/IUBMB notation commonly used to represent unmodified DNA, RNA, and proteins to describe non-canonical forms of DNA, RNA, and proteins. Features include the representation of a wider range of monomeric forms, incl ...

GAIA (G-quAdruplexes In Alive creature) is a user-friendly database with a web interface that can be used to query a data set containing pG4s in diverse species from all three living kingdoms.

This Web resource provides data and information relevant to SARS coronavirus. It includes links to the most recent sequence data and publications, to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates ...

MozAtlas provides gene expression data of adult male and female mosquitoes as tables, expressions, trees and models. MozAtlas also provides sequence orthology relationships with data provided by FlyBase, Vectorbase, Beetlebase, BeeBase, and WormBase.

A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.

!!! >>> the repository is offline >>> !!! GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on represent ...

This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Datab ...

SimTK is a free project-hosting platform for the biomedical computation community that enables researchers to easily share their software, data, and models and provides the infrastructure so they can support and grow a community around their projects ...

The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, functi ...

<<<!!!<<< This repository is no longer available. >>>!!!>>> The main objective of our work is to understand the pathomechanisms of late onset neurodegenerative disorders such as Huntington's, Parkinson's, Alzheimer's and Machado Joseph disease and to ...

The organelle genomes are part of the NCBI Reference Sequence (RefSeq) project that provides curated sequence data and related information for the community to use as a standard.