Tag: plant


Found 130 sources
Source Match ReputationScore*

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants


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 ...
100%

Phytozome


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 ...
96%

Brassica Genome


This site hosts Brassica genome databases.
91%

Antimicrobial Peptide Database


The data stored in the APD are gleaned from the Protein Data Bank (PDB), Swiss-Prot Protein Knowledgebase and PubMed National Library of Medicine. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the matur ...
86%

Plant Transcription Factor Database


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 ...
85%

Sol Genomics Network


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.
83%

PLAZA


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.
82%

CottonGen


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 ...
80%

Maize Genetics and Genomics Database


MaizeGDB is the maize research community's central repository for genetics and genomics information.
80%

SoyBase


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 ...
80%

PLEXdb


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 ...
79%

Genome Database for Rosaceae


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.
78%

Plant Ontology


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 ...
77%

Arabidopsis Information Portal


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 ...
77%

Genetic and Genomic Information System


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, ...
76%

Arabidopsis Thaliana Trans-factor and cis-Element prediction Database


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 ...
72%

PhosPhAt


Arabidopsis Protein Phosphorylation Site Database
71%

ARAMEMNON


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 ...
71%

AgBase


AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.
70%

Database of Arabidopsis Transcription Factors


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 ...
70%

The Arabidopsis Gene Regulatory Information Server


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 ...
69%

Plant DNA C-values database


A database containing genome size (C-value) data for all groups of land plants and red, green and brown algae.
67%

Plant Resistance Gene Database


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.
66%

GREENC


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 ...
66%

US Department of Energy Systems Biology Knowledgebase


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 ...
65%

Tomato Functional Genomics Database


The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.
65%

Panzea


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.
65%

GreenPhylDB: A phylogenomic database for plant comparative genomics


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.
64%

RiceXPro


Rice transcriptome under natural conditions
64%

Information Commons for Rice


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 ...
63%

LegumeIP


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.
63%

Database of Rice Transcription Factors


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 ...
63%

MetaCrop 2.0


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. ...
63%

Leaf Senescence Database


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.
62%

Plant Natural Antisense Transcripts Database


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 ...
62%

Plant Promoter Database


Genome-wide plant promoter database for several plant species, including Arabidopsis thaliana, rice, poplar, and Physcomitrella patens.
61%

Beijing Genomics Institute Rice Information System


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 ...
61%

Shanghai Rapeseed Database


Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica.
61%

BarleyBase


BarleyBase is a public data resource of Affymetrix GeneChip data for plants.
59%

Soybean Knowledge Base (SoyKB)


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 ...
59%

PAIR


Predicted Arabidopsis Interactome Resource
58%

CR-EST - Crop ESTs


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 ...
58%

Arabidopsis Hormone Database


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 ...
58%

PLANT-PIs


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 ...
57%

TropGENE DB


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.
57%

GrainGenes, a Database for Triticeae and Avena


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 ...
57%

Coffee Genome Hub


Coffee community genomics, genetics and breeding data and analysis tools
57%

PmiRKB


Plant microRNA knowledge base
56%

Oryza Tag Line


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.
56%

autoSNPdb


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 ...
56%

AtPID


Arabidopsis thaliana Protein Interactome Database
56%

Manually Curated Database of Rice Proteins


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 ...
55%

OryGenesDB: an interactive tool for rice reverse genetics


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 ...
55%

AraPheno


Phenotypic data for Arabidopsis thaliana
54%

Plant Reactome


Plant metabolic, regulatory and signaling pathways
53%

GoMapMan


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.
52%

NIAS


Databases for genetic resources and plant disease information
52%

GabiPD


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 ...
46%

PlantGDB


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 ...
43%

PlantDHS


Plant DNase I hypersensitive Site Database
43%

PlantPAN


Plant Promoter Analysis Navigator
43%

PlantProm


Plant promoter sequences
43%

Plant MPSS


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 ...
43%

PlantTribes


Families of protein-coding genes from five sequenced plant species
43%

Plant snoRNA DB


snoRNA genes in plant species
43%

PlantsP/PlantsT


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 ...
43%

Plant Metabolomics


Arabidopsis metabolomics database
43%

Plant repeat database


Repetitive sequences in plant genomes
43%

Plant Stress-Responsive Gene Catalog


Stress-responsive gene in various plant species
43%

PathoPlant®


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 ...
43%

MIPSPlantsDB


MIPS Plants Databases
43%

POGs/PlantRBP


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 ...
43%

GÉnoPlante-Info


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 ...
43%

PPDB: Plant Proteomics Database


Plant Proteomics Database
43%

TIGR Plant Transcript Assembly 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 ...
43%

P3DB


Plant protein phosphorylation database
43%

PGDD


Plant Genome Duplication Database
43%

PNRD


Plant Non-coding RNA Database
43%

PMDBase


Plant microsatellites and marker development
43%

PIECE


Plant Intron Exon Comparison and Evolution
43%

DRASTIC


Database resource for analysis of signal transduction in plant cells
43%

PhytAMP


Data repository of plant natural antimicrobial peptides
43%

PHYTOPROT


Clusters of predicted plant proteins
43%

PLaMoM


Plant Mobile Macromolecules: Extracellular siRNAs, microRNAs, mRNAs and proteins in plants
43%

P-MITE


Plant miniature inverted-repeat transposable elements (MITEs)
43%

AraNet


Functional relationships between plant genes
43%

MAtDB2


MIPS Arabidopsis thaliana database
43%

PceRBase


Competing endogenous RNAs in plants
43%

EURISCO


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 ...
43%

TAED - The Adaptive Evolution Database


A phylogeny-based tool for comparative genomics
43%

Plastid-LCGbase


Plastid Lineage-based Conserved Gene-pair Database
43%

SeedGenes


Genes essential for Arabidopsis development
43%

MOsDB


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) ...
43%

RiceGAAS


Rice genome automated annotation system
43%

RiceVarMap


Rice Variation Map, SNPs and indels
43%

SUBA


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 ...
43%

RiceFREND


Rice Functionally Related gene Expression Network Database
43%

PLprot


Arabidopsis thaliana chloroplast protein database
43%

Rice Gene Thresher


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 ...
43%

Rice Pipeline


Unification tool for rice databases
43%

GEM2Net


Arabidopsis thaliana genes involved in stress response
43%

GETPrime


Gene- or transcript-specific primers for qPCR
43%

AthaMap


Genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana
43%

ccNET


Co-expression networks for diploid and polyploid Gossypium
43%

SoyNet


Co-functional networks for soy bean, Glycine max
43%

FLOR-ID


Flowering Interactive Database
43%

NASCarrays (obsolete)


Nottingham Arabidopsis Stock Centre microarray database
43%

Arabidopsis MPSS


Arabidopsis gene expression detected by massively parallel signature sequencing
43%

Chloroplast Genome Database


Chloroplast genome database
43%

Rice Mutant Database


Rice mutant database
43%

GABI-Kat SimpleSearch 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 ...
43%

Medicago trunculata Database


Medicago trunculata-related resources
43%

Rice Proteome Database


Rice proteome database
43%

Arabidopsis Mitochondrial Protein Database


Experimentally identified mitochondrial proteins in Arabidopsis
43%

Rice Annotation Database


Contig data for manual annotation of rice genome
43%

CATMA - Complete Arabidopsis Transcriptome MicroArray


Arabidopsis gene sequence tags
43%

Arabidopsis Nucleolar Protein Database


Comparative analysis of nucleolar proteomes of human and Arabidopsis
43%

RARGE - RIKEN Arabidopsis Genome Encyclopedia


Arabidopsis cDNAs, mutants and microarray data
43%

Diatom EST Database


ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum
43%

ASRP - Arabidopsis Small RNA Project


Arabidopsis thaliana small RNA project
43%

AtGDB


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 ...
43%

Cereal Small RNA Database


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 ...
43%

MPIM - Mitochondrial Protein Import Machinery


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 ...
43%

RetrOryza


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 ...
43%

PoMaMo - Potato Maps and More


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 ...
43%

ForestTreeDB


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 ...
43%

TIGR Maize database


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 ...
43%

RAP-DB


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 ...
43%

SNP-Seek


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 ...
43%

TomatEST DB


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 ...
43%

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