Tag: plant biology

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 Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxo ...

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as s ...

Database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.

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 ...

Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 5 ...

MaizeGDB is the maize research community's central repository for genetics and genomics information.

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 ...

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...

The Dfam database is a open collection of DNA Transposable Element sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. Dfam represents a collection of multiple sequence alignments, each containing a set of r ...

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...

ATTED-II is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can find functional gene relationships and design experiments to identify gene functions by reverse gene ...

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

MoonProt Database is a manually curated, searchable, internet-based resource with information about the over 200 proteins that have been experimentally verified to be moonlighting proteins. Moonlighting proteins comprise a class of multifunctional pr ...

The Carbohydrate Structure Database (CSDB) contains manually curated natural carbohydrate structures, taxonomy, bibliography, NMR data and more. The Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases were merged in 2015, becoming the CSDB, to impr ...

Arabidopsis Protein Phosphorylation Site Database

We developed a pipeline to annotate lncRNAs (Long non-coding RNAs) and applied it to 37 plant species and six algae, resulting in the annotation of more than 120 000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the in ...

ARAMEMNON is a curated database for Arabidopsis thaliana transmembrane (TM) proteins and transporters. The database compiles topology and signal sequence predictions and displays the results in a directly comparable graphical output format for presen ...

AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regula ...

The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and anno ...

miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mi ...

PRGdb is an open and daily updated space about plant resistance genes, in which all information about this family is stored, curated and discussed. This resource encourages research community curation of plant resistance genes.

The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and in ...

Genome-wide plant promoter database for several plant species, including Arabidopsis thaliana, rice, poplar, and Physcomitrella patens.

GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.

Rice transcriptome under natural conditions

The Leaf Senescence Database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. LSD includes data types such as leaf senescence-associated transcriptomics, phenotype and interaction data.

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.

GBIF, the Global Biodiversity Information Facility, is an international open data infrastructure, funded by governments. It is not a data repository. Rather, GBIF indexes thousands of datasets shared freely by hundreds of institutions worldwide makin ...

The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. ...

The compendium of crop Proteins with Annotated Locations (cropPAL) collates more than 550 data sets from previously published fluorescent tagging or mass spectrometry studies and eight pre-computed subcellular predictions for barley, wheat, rice and ...

The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and ...

Customizable RNA-seq Data Analysis and Visualization Platform.

Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform fo ...

The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant ima ...

DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences a ...

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 ...

This database contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples).

Coexpressed genes and networks in human and mouse

The crop EST database CR-EST (http://pgrc.ipk-gatersleben.de/cr-est/) is a publicly available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at IPK Gatersleben, Germany. CR-EST curre ...

Plant protease inhibitors (PIs) can be counted among the defensive proteins that plants display to minimize the adverse effects deriving from the attack of phytophagous insects. They are usually present in seeds and storage tissues, but are also expr ...

COPO is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile. By tracking unique id ...

Coffee community genomics, genetics and breeding data and analysis tools

Biosynthetic gene cluster families

Plant microRNA knowledge base

Plant metabolic, regulatory and signaling pathways

Phenotypic data for Arabidopsis thaliana

It is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 spec ...

PmiREN is a comprehensive encyclopedia of plant miRNAs.

Integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.

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

Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.

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 ...

The Tobacco Markers & Primers Database.

OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...

Gephebase is a manually-curated database compiling our accumulated knowledge of the genes and mutations that underlie natural, domesticated and experimental phenotypic variation in all Eukaryotes — mostly animals, plants and yeasts. Gephebase conso ...

Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots | A platform dedicated to the visualization and analysis of plant co-expression and co-function networks

PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables user ...

A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling t ...

PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including ...

Comprehensive database of transposable elements in conifers.

A database for the integration and access to knowledge on host-symbiont relationships.

A chemical data resource with relational data between natural products and biological sources. NPBS Database of Shanghai Institute of Organic Chemistry.

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.

Arabidopsis thaliana Multi-omics Association Database

TarDB is a database for conserved miRNA targets, degradome supported miRNA targets and miRNA-triggered phasiRNAs in plants. TarDB is a plant miRNA target repository, which is based on cross-species conservation filter, degradome PARE-seq, and small R ...

The Plant Experimental Assay Ontology (PEAO) was created to describe experimental procedures within plant research, regardless of the scientific questions that prompted the assays. This ontology models entities from three distinct realms (biological, ...

Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.

CpGDB (Chloroplast Genome Database) is a user friendly, freely available and dynamic relational database which allows search and download of complete chloroplast genome sequences, individual gene sequences and feature records of different plant speci ...

Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables

A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.

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

A database for plant circRNAs that act as miRNA decoys. Circular RNAs (circRNAs) are a novel type of RNAs that form covalently closed loop structures with neither 5'- 3' polarities nor polyadenylated tails. GreenCircRNA(v1.0) is the most comprehensi ...

Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis | Non-specific lipid transfer protein structure modeling | Theoretical structures have been calculated for the ...

The CGDB (Coriander Genome Database) is mainly contained the coriander genome, transcriptome, and metabolome datasets

A toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL is a tool to cluster and extract summarized associations of Gene Ontology based functions in omics data. It clusters GO terms using MCL ba ...

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 ...

SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500.

CuAS is an integrated database for Cucumber Alternative Splicing, includes genomic annotation, isoform-level functions, isoform-level features and tissue-specific AS events among multiple tissues.

FlorItaly is a data portal for the flora of Italy. This portal organises nomenclatural and distributional data from the recent checklists of the Italian native and alien vascular plants (and their subsequent updatings), with links to resources from o ...

WARPP is the Web Application for the Research of Parasitic Plants, a community hub for access, information sharing and analysis of parasitic plant-specific data. The aim of this resource is to facilitate international efforts for the study of parasit ...

A comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.

An online database for exploring over 2,000 Arabidopsis small RNA libraries.

TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.

A large-scaled depository of mass spectrometry datasets for metabolome analysis.

scAPAdb provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level in six species based on a large volume of scRNA-seq data. Currently, scAPAdb records APA information in animal speci ...

A database for construction and analysis of functional interaction networks for any species with a sequenced genome. Earth BioGenome Project has been officially launched in November 2018 with the goal of decoding genomes of Earth’s biome over a peri ...

PlaSMo stands for Plant Systems-biology Modelling and the mission of the project was ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

A host-pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms.

CANNUSE is a database containing the traditional uses of Cannabis.

An integrative database of quantitative post-translational modifications in plants.

The SistematX Web Portal of Natural Products is database of secondary metabolites.

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

Database for the mulberry metabolome. The Mulberry Metabolome Database. Comprehensively, freely, and User-friendly.

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

CSDB_GT, a curated glycosyltransferase database with close-to-full coverage on three most studied non-animal species.

FermFooDb is a database of peptides derived from fermented foods contains 2325 entries of unique peptides from the fermented foods.

The Virtual Herbarium ALTB (Russian interface ) is the largest digital collection of plants from the transboundary territory of the Altai Mountain Country

Is an online platform focuses on providing an up-to-date account of Botryosphaeriales with notes on orders, families and genera and species, keeping abreast of the current literature.

Expansin Engineering Database integrates information on sequence, structure and function of expansins.

ResiDB is a user-friendly sequence similarity-dependent database manager for bacteria, fungi, viruses, protozoa, invertebrate, plants, archaea, environmental and whole genome shotgun sequence data. Create a new database Access existing databases Loa ...

An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biologi ...

The purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world. The web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an imple ...

The plant sRNA portal is a a database of annotated sRNAs integrating the miRPursuit pipeline to identify, predict and annotate plant small RNAs (sRNA).

Integrative database around plant genomes.

Plant transfer RNA database.

Database of plant protein inter-cultivar variability and function.

Plant cytochrome P450 database and web-based tools for structural construction and ligand docking. It is a reliable template-based structure prediction method (PCPCM), and predicted the structures of 180 plant P450s with known functions. In addition, ...

A curated and comprehensive resource of plant cell markers.

A database for the molecular weight and isoelectric points of the plant proteomes.

Web-based platform of nucleotide sequence alignments of plants.

An integrative database for traditional Chinese medicine plant genomes.

Full-length transcripts and conservation of plant circRNAs.

Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.

Structural and functionnal annotation of plant gene and protein families by a network of experts.

A database for orchid genomics and molecular biology.

Plant transfer RNA-derived non-coding RNAs (tncRNAs) database.

A platform for virtual screening and computer-aided drug designing.

A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication.

The Database of Pollinator Interactions (DoPI) documents British pollinator-plant associations.

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

A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem.

A comprehensive resource for kiwifruit genomics.

Rcompadre and Rage are two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models. It is an R package to facilitate working with the COM(P)ADRE Plant and Animal Matr ...

Database of circadian and ultradian transcripts in control tissues of kingdom-wide species.

Methods for broad-scale plant phenology assessments using citizen scientists’ photographs | iNaturalist.org is a joint initiative of the California Academy of Sciences and the National Geographic Society | Explore and share your observations from the ...

Plant Repeat Database (Plantre) provides re-annotated repeat sequences of plant using a uniform pipeline. The current version of plantrep contains 206.04Gb of 396,041,410 repeats from 459 species that were divided into 15 clades based on their phylog ...

An integrated multi-omics database of barley gene families.

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

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants.

A subcellular localisation database for Arabidopsis proteins, with online search interface.

A comprehensive genome platform for Brassicaceae plants.

FAIDARE: FAIR Data-finder for Agronomic Research. The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories. It is based on the Breeding API (BrAPI) specificat ...

A global tree allometry and crown architecture database.

Biologer is an open platform for collecting biodiversity data.

A web-based tool to access and analyse bacterial pesticidal proteins.

A comprehensive database of long inverted repeats in eukaryotic genomes.

Database of Cork Oak EST sequences from the Portuguese Cork Oak sequencing project.

A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.).

A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life.

HORDB a comprehensive database of peptide hormones.

An open source database(s) for genetics, genomics and functional research in rice species

An Open Access Data Repository of Mass Spectra for Chemical Ecology.

A comprehensive database for alternative splicing in tea plants (Camellia sinensis).

a database repository of uniformly-annotated small RNAs in plants | Abstract Small RNAs (sRNAs) are essential regulatory molecules, including three mayor classes in plants, microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs ...

A Comprehensive Multi-Omics Association Database of Secondary Growth in Response to Stress in Populus trichocarpa.

A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease.

AlnC is an extensive database of long non-coding RNAs in Angiosperms.

Stress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network.

A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.

A comprehensive repetitive sequence database of over 80 000 species.

ConnecTF is a platform to build gene networks by integrating transcription factor-target gene interactions.

DataBase of Plant Research (DBHR) is an online data resource specifically designed for human research, which provides access to almost all latest human database on easy and friendly finding way, the classification based on data type is informative an ...

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

MPDB 2.0 contains more than 500 indigenous medicinal plants of Bangladesh. It encompasses the plants scientific name, family name, local names, utilized parts, active compounds and the PubMed IDs of related articles.

Gene Expression platform to investigate gene expression and functionalities in the tomato genome. It includes expression data from cultivated specie/variety Heinz 1706, Ailsa Craig e Solanum pimpinellifolium.

Gene Ontology Meta Annotator for Plants. Lawrence-Dill Plant Informatics and Computation Lab. Welcome to GOMAP-singularity’s documentation! — GOMAP-Singularity 1.3.2 documentation. All publications and products by the team at Lawrence-Dill Plant I ...

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 ...

A comparative platform on grapevine and tomato reporting paralog and related ortholog genes identified with an analytical, dedicated, procedure. It provides an update on functional annotations from the two species and it represents an internationally ...

This project aims at building an International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-access web based system to access to the available data resources and bioinformatics ...

An Expanded Database of Ecological and Phenotypical Features of Microbes. Microbial communities are an incredibly fascinating and genetically diverse set of organisms that live with us, in us, and around us! Explore them all using the Microbe Direct ...

Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

A novel approach for validation and completeness of protein orthologous groups. A novel approach for validation and enrichment of protein orthologous groups. KusakiDB is a database of protein orthologous groups (OGs) that:.

A web-based application for molecular identification of Prototheca species.

MedProDB is the first database dedicated to Mediator protein in plants, fungi and animals. It harbors 33,971 entries of different types of Mediator subunits of various organisms. This database is believed to be beneficial for exploring the complex an ...

RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultiva ...

TCM-Blast for traditional Chinese medicine genome alignment with integrated resources.

A method of using global evidence for local decision making. Metadataset (www.metadataset.com) is a collection of open data from scientific publications. These publications are about the management of agricultural and natural resources (e.g., crops, ...

A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS). Developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The datab ...

A database storing SNPs and their predicted impact on transcription factor (TF) binding in promoter regions for different crops.

Co-expression Network Database for <i>de novo</i> Transcriptome Assembly of <i>Paeonia lactiflora</i> Pall. Paeonia lactiflora Pall., commonly known as the herbaceous peony, is an ornamental flowering plant known around the world. Its oil contains a ...

A Functional Analysis Tools for Post-translational Modifications (FAT-PTM) database, which supports data from publicly available proteomic analyses encompassing eight different types of PTMs and over 49,000 PTM sites.

Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo scrip ...