Tag: plant biology


Found 97 sources
Source Match ReputationScore*

JASPAR


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 ...
100%

The Arabidopsis Information Resource


The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
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 ...
97%

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 ...
96%

Gene Ontology Annotation Database


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 ...
89%

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 ...
86%

Maize Genetics and Genomics Database


MaizeGDB is the maize research community's central repository for genetics and genomics information.
81%

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 the most current genetic, physical and genomic sequence maps integrat ...
81%

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 ...
81%

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, ...
77%

Legume Information System


The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.
74%

PhosPhAt


Arabidopsis Protein Phosphorylation Site Database
72%

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 ...
72%

AgBase


AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.
72%

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 ...
71%

PlnTFDB


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 ...
70%

miRNEST


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 ...
69%

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.
68%

JGI Genome Portal


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 ...
67%

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.
66%

RiceXPro


Rice transcriptome under natural conditions
65%

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.
64%

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. ...
64%

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 ...
63%

Global Biodiversity Information Facility


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 ...
63%

Plant MicroRNA Database (PMRD)


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 ...
63%

CropPAL


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 ...
62%

Oryzabase


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 ...
62%

Description of Plant Viruses


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 ...
61%

FGDB


Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the ...
61%

Complete Arabidopsis transcriptome database


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).
61%

COXPRESdb


Coexpressed genes and networks in human and mouse
61%

expVIP


Customizable RNA-seq Data Analysis and Visualization Platform.
61%

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 ...
59%

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 ...
59%

Collaborative Open Plant Omics


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 ...
58%

Coffee Genome Hub


Coffee community genomics, genetics and breeding data and analysis tools
58%

PmiRKB


Plant microRNA knowledge base
58%

LSD


This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to their functions in leaf sene ...
57%

SALAD


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 ...
57%

AraPheno


Phenotypic data for Arabidopsis thaliana
56%

Sinbase


Integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.
55%

Structural and functional annotation of Arabidopsis thaliana gene and protein families


GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.
55%

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.
54%

Plant Reactome


Plant metabolic, regulatory and signaling pathways
54%

NBRP resources


System for collecting, preserving and providing bioresources for use as experimental materials for life science research.
54%

AlgaePath


Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.
53%

CoNekT-Plants


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
52%

TMPD


The Tobacco Markers & Primers Database.
52%

SymbioGenomesDB


A database for the integration and access to knowledge on host-symbiont relationships.
51%

PlantCircNet


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 ...
51%

AtMAD


Arabidopsis thaliana Multi-omics Association Database
51%

Gephebase


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 ...
51%

ConTEdb


Comprehensive database of transposable elements in conifers.
51%

MBKbase rice


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 ...
51%

Plant Experimental Assay Ontology


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, ...
51%

PmiREN


PmiREN is a comprehensive encyclopedia of plant miRNAs.
51%

PlantAPAdb


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 ...
51%

VegMarks


Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables
50%

PEATmoss


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 ...
50%

PCIR


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 ...
49%

nsLTP


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 ...
49%

PSRN


Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.
48%

PlaSMo


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.
48%

ASRD


An online database for exploring over 2,000 Arabidopsis small RNA libraries.
48%

RsHSF


Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.
48%

BacHBerryEXP


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.
48%

SEQdata-BEACON


SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500.
48%

BiomeNet


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 ...
48%

LeGOO


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 ...
48%

Plant DataDiscovery


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 ...
44%

sRNA plant portal


The plant sRNA portal is a a database of annotated sRNAs integrating the miRPursuit pipeline to identify, predict and annotate plant small RNAs (sRNA).
44%

FLAGdb


Integrative database around plant genomes.
44%

PhytoTypeDB


Database of plant protein inter-cultivar variability and function.
44%

PlantAligDB


Web-based platform of nucleotide sequence alignments of plants.
44%

SCMVTDb


Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.
44%

PlantCARE


Database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
44%

iNaturalist


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 ...
44%

TRANSNAP


TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.
44%

SUBA3


A subcellular localisation database for Arabidopsis proteins, with online search interface.
44%

FAIDARE


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 ...
44%

CorkOakDB


Database of Cork Oak EST sequences from the Portuguese Cork Oak sequencing project.
44%

GenOrigin


A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life.
44%

Rice Genome Hub


An open source database(s) for genetics, genomics and functional research in rice species
44%

sRNAanno


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 ...
44%

NexGenEx-Tom


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.
44%

GreenCircRNA


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 ...
44%

GOMAP


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 ...
44%

ComParaLogS


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 ...
44%

WheatIS


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 ...
44%

Microbe Directory


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 ...
44%

Genomicus-plants


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.
44%

RARe


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 ...
44%

ProMEX protein mass spectral library


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 ...
44%

HpeNet


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 ...
44%

GOMCL


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 ...
44%

GenomeHubs


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 ...
44%

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