RESOURCESRESOURCES

Genome Databases

Central repositories, genome browsers and databases that collate and display information relating to Arabidopsis and other plants genomes.

AgriGO

http://bioinfo.cau.edu.cn/agriGO/

The agriGO is a web-based tool and database for the gene ontology analysis. It supports specicial focus on agricultural species and is user-friendly.

The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are:

ARAPORT

https://www.araport.org/

Arabidopsis Genome Database, a NSF-BBSRC funded resource. Loads of useful tools so take time to explore!

Chloroplast Genome Database

http://chloroplast.cbio.psu.edu/

This database contains annotated chloroplast/plastid genomes from the NCBI Organelle Genomes section at NCBI. You can search for genes by their annotated names, conduct flexible BLAST searches, download protein and nucleotide sequences extracted from a selected chloroplast genome, and browse the putative protein families (tribes) created using TribeMCL.

Ensembl Plants

http://plants.ensembl.org/index.html

A web resource for plant genomics research, including browsers for Arabidopsis spp., rice, tomato,  and other species. 

FLAGdb++

http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/index.shtml

FLAGdb++helps users to understand the biological role of plant genes by considering them in a wide context: a multigene family, a topological environment, and/or a functional network.

From the abstract: The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches.

Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera).

FrameOPT

http://www.mcr.org.in/frameopt/

A database containing the optimal codons in different plant species. Codon usage bias (CUB) is an important phenomenon to understand the kinetics of protein translation machinery and for modulating the expression of transgenes through codon optimization. It also provides an overview of the evolutionary dynamics underlying diversity across living organism genera, phyla or classes.

GEMMA

http://www.chibi.ubc.ca/Gemma/home.html;jsessionid=D1D347293DA71BC567F8C907DC500A13

Test for co-expression or differential expression of genes in different experiments. An existing database of over 3300 expression profiling studies which can be user-updated. 

From the abstract: Gemma is a database, analysis software system and web site for genomics data re-use and meta-analysis. Gemma currently contains analysed data from over 3300 expression profiling studies, yielding hundreds of millions of differential expression results and coexpression patterns (correlated expression) for retrieval and visualisation.

iRootHair

http://www.iroothair.org/

iRootHair is a unique resource for root hair research that integrates the large volume of data related to root hair genomics in a single, curated, expandable, and freely available database.

Text taken from the abstract of the iRootHair paper, by Kwasniewski et al. (Plant Phys. 2012; 161:28-35)

 

MAtDB

http://mips.helmholtz-muenchen.de/plant/athal/

MAtDB started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project, part of the Arabidopsis Genome Initiative, but is moving towards becoming an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities. The aim is to create a comprehensive resource for Arabidopsis as a model that can then be used to transfer knowledge onto sequences from other species, including crop plants.

Plant Genome Duplication database

http://chibba.agtec.uga.edu/duplication/

PGDD is a public database to identify and catalog plant genes in terms of intragenome or cross-genome syntenic relationships. Current efforts focus on flowering plants with available whole genome sequences (preferrably assembled pseudomolecules with ordered gene models).

Planteome

http://www.planteome.org/

The cROP project is a heavily collaborative project that depends on coordination with several national and international projects. Existing and new collaborations are of following four types:

> Development and enrichment of new and existing reference ontologies for plants.

> Ontology use. Annotating the gene expression profiles and phenotypes in OMICs and Tree of Life projects and sharing the annotations with cROP data warehouse.

> Ontology cros-references. Project collaborators will continue to use the ontologies developed as part of the cROP initiatives as a reference vocabularies to map terms from similar vocabularies described or already in use by various plant databases and individual research projects - thereby creating a semantic web of ontologies required for plant biology.

> Develop data annotation standards. We will engage in close collaboration with the various plant genome sequencing and annotation projects as well as with the comparative genomics databases such as Gramene, Interpro, Uniprot, EBI-ArrayExpress/ATLAS, PlantEnsembl, PLEXdb, DOE-KnowledgeBase, NSF-Phenotype-RCN, iPlant, etc.

 

PlantGDB

http://www.plantgdb.org/

The plantgdb.org web resource aims to develop robust genome annotation methods, tools, and standard training sets for the plethora of plant genomes currently or soon to be sequenced. The tools include special datasets for transposon insertion sites and lists of useful resources for genomics. 

PLAZA

https://bioinformatics.psb.ugent.be/plaza/

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics.

TAIR

http://www.arabidopsis.org/

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 product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.

transPLANT

http://www.transplantdb.eu/

transPLANT is a consortium of 11 European partners gathered to address these challenges and to develop a trans-national infrastructure for plant genomic science. Bringing together groups with strengths in data analysis, plant science, computer science, and from the academic and commercial sectors. transPLANT will develop integrated standards and services, undertaking research and development to capitalise on the sequencing revolution across the spectrum of agricultural and model plant species.

EU-funded umbrella organisation that includes Ensembl Plants.

Large amount of genome information on the website so take some time to have a look around!