Tag: plant

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 ...

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 ...

This site hosts Brassica genome databases.

The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The anti ...

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 ...

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 ...

PLAZA is a platform for comparative, evolutionary, and functional genomics. The platform consists of multiple instances, where each instance contains additional genomes, improved genome annotations, new software tools, etc.

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 ...

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...

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 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.

The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plant ...

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 ...

KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase ...

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 Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arab ...

A database containing genome size (C-value) data for all groups of land plants and red, green and brown algae.

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.

Panzea provides information on the connection between phenotypes and genotypes of complex traits in maize and its wild relative, teosinte, and specifically in how rare genetic variations contribute to overall plant function.

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

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

Information Commons for Rice (IC4R) is a rice knowledgebase that incorporates rice data through multiple modules such as genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequen ...

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.

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. ...

DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF incl ...

Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica.

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 ...

In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The database has annotated the rice genomes for gene content, repetitive elements, and SNPs. Sequence polymorphis ...

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 ...

Soybean Knowledge Base (SoyKB), is a comprehensive all-inclusive web resource developed for soybean translational genomics and molecular breeding. SoyKB stores information about genes/proteins, miRNAs/sRNAs, metabolites, SNPs, plant introduction (PI ...

BarleyBase is a public data resource of Affymetrix GeneChip data for plants.

Predicted Arabidopsis Interactome Resource

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including au ...

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 ...

TropGENE DB is a database that manages genetic and genomic information about tropical crops studied by Cirad. The database is organised into crop specific modules.

Coffee community genomics, genetics and breeding data and analysis tools

Plant microRNA knowledge base

Plant metabolic, regulatory and signaling pathways

Phenotypic data for Arabidopsis thaliana

Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library.

Implemented the SNP discovery software autoSNP within a relational database to enable the efficient mining of the identified polymorphisms and the detailed interrogation of the data. AutoSNP was selected because it does not require sequence trace fil ...

Arabidopsis thaliana Protein Interactome Database

The Manually Curated Database of Rice Proteins (MCDRP) is a manually-curated database based on published experimental data. The database contains data for rice proteins curated from experiments drawn from research articles. The database stores inform ...

The aim of this Oryza sativa database was first to display sequence information such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. This ...

Databases for genetic resources and plant disease information

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.

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary in ...

RIKEN BRC collects, preserves and distributes five important bioresources: experimental mouse strains, Arabidopsis thaliana and other laboratory plants, cultured cell lines of human and animal origin, microorganisms, genetic materials of human, anima ...

Plant DNase I hypersensitive Site Database

Plant Promoter Analysis Navigator

PlantGDB is a database of plant genomic sequences, in particular Expressed Sequence Tags (ESTs) that correspond to fragments of genes that are actively transcribed under particular conditions. For each of 48 species, the database organizes the ESTs i ...

Plant promoter sequences

MPSS (Massively Parallel Signature Sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. The Plant MPSS databases are the largest publicly ava ...

Families of protein-coding genes from five sequenced plant species

snoRNA genes in plant species

As one database with two functionally different web interfaces, PlantsP and PlantsT are plant-specific curated databases that combine sequence derived information with experimental functional genomics data. PlantsP focuses on proteins involved in the ...

Arabidopsis metabolomics database

Repetitive sequences in plant genomes

Stress-responsive gene in various plant species

PathoPlant® has been developed as a relational database to display relevant components and reactions involved in signal transduction related to plant-pathogen interactions. Signal transduction pathways are modeled as consecutive sequences of known m ...

MIPS Plants Databases

POGs/PlantRBP (http://plantrbp.uoregon.edu/) is a relational database that integrates data from rice, Arabidopsis, and maize by placing the complete Arabidopsis and rice proteomes and available maize sequences into "putative orthologous groups" (POGs ...

GÉnoplante is a collaboration between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sun ...

Plant Proteomics Database

The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed Sequenc ...

Plant protein phosphorylation database

Plant Genome Duplication Database

Plant Non-coding RNA Database

Plant microsatellites and marker development

Plant Intron Exon Comparison and Evolution

Database resource for analysis of signal transduction in plant cells

Data repository of plant natural antimicrobial peptides

Clusters of predicted plant proteins

Plant Mobile Macromolecules: Extracellular siRNAs, microRNAs, mRNAs and proteins in plants

Plant miniature inverted-repeat transposable elements (MITEs)

Functional relationships between plant genes

MIPS Arabidopsis thaliana database

Competing endogenous RNAs in plants

The European Search Catalogue for Plant Genetic Resources (EURISCO) provides informationabout more than 2 million accessions of crop plants and their wild relatives, preserved ex situ by almost 400 institutes. It is based on a network of National Inv ...

A phylogeny-based tool for comparative genomics

Plastid Lineage-based Conserved Gene-pair Database

Genes essential for Arabidopsis development

MOsDB (http://mips.gsf.de/proj/plant/jsf/rice/index.jsp) is a resource for publicly available sequences of the rice (Oryza sativa L.) genome. Our goal at MOsDB is to provide all available data about rice genes and genomics, including (in the future) ...

Rice genome automated annotation system

Rice Variation Map, SNPs and indels

The Arabidopsis Subcellular Database (SUBA, http://suba.plantenergy.uwa.edu.au) is maintained by the ARC Centre of Excellence in Plant Energy Biology at The University of Western Australia. The database contains publicly available protein subcellular ...

Rice Functionally Related gene Expression Network Database

Arabidopsis thaliana chloroplast protein database

RiceGeneThresher is a public online resource for mining genes underlying genome regionsof interest or quantitatie trait loci (QTLs) in the rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, EST ...

Unification tool for rice databases

Arabidopsis thaliana genes involved in stress response

Co-expression networks for diploid and polyploid Gossypium

Gene- or transcript-specific primers for qPCR

Genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

Co-functional networks for soy bean, Glycine max

Flowering Interactive Database

Nottingham Arabidopsis Stock Centre microarray database

Arabidopsis gene expression detected by massively parallel signature sequencing

Chloroplast genome database

Rice mutant database

Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generate ...

Medicago trunculata-related resources

Rice proteome database

Experimentally identified mitochondrial proteins in Arabidopsis

Contig data for manual annotation of rice genome

Arabidopsis gene sequence tags

Comparative analysis of nucleolar proteomes of human and Arabidopsis

Arabidopsis cDNAs, mutants and microarray data

ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum

Arabidopsis thaliana small RNA project

AtGDB is being developed as a part of our NSF-funded project "PlantGDB - Plant Genome Database and Analysis Tools". The purpose of this resource is to provide a convenient sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on ...

Small RNAs (smRNAs), which include microRNAs (miRNAs), small-interfering RNAS (siRNAs) and trans-acting siRNAs (ta-siRNAs) are ~19-24 nt RNAs that are important negative regulators of nucleotide sequences involved in development, homeostasis and in t ...

Mitochondrial protein import is essential for mitochondrial function, and thus the viability of most eukaryotic life, yet it has been characterized in only a few organisms. The Mitochondrial Protein Import Machinery (MPIM) database contains informati ...

With the availability of the complete genomic sequence of rice, the identification and annotation of LTR-Retrotransposons has become a necessity as they comprise an important part of plant genomes (1). RetrOryza is a database that aims at providing t ...

The database PoMaMo (Potato Maps and More) was established within the German Plant Genome Project "GABI". It harbours to date information on molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene ...

ForestTreeDB is intended as a resource that centralizes large-scale EST sequencing results from several tree species (http://foresttree.org/ftdb). Our group at the Center for Computational Genomics and Bioinformatics (University of Minnesota) aims to ...

The TIGR Maize Database is a repository of publicly available maize genomic sequences, we have created the TIGR Maize Database (http://maize.tigr.org). In this resource, we have assembled approximately 900,000 gene-enriched reads into Assembled Zea m ...

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was h ...

The Rice SNP-Seek Database features SNP data from various cultivars alongside the Nipponbare reference genome: IR 64, 93-11, DJ 123 and Kasalath. Genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse ...

TomatEST is a secondary database integrating EST/cDNA sequence information from different libraries of multiple tomato species collected from dbEST. Redundant EST collections from each species are organized into clusters (gene indices). A cluster con ...