Arabidopsis thaliana Tools and Portals
- TAIR
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TAIR, the Arabidopsis Information Resource, is a genetic and molecular biology resource for Arabidopsis thaliana created by the Arabidopsis Biological Resource Center at the Ohio State University.
- Cis-BP
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Cis-BP, the Catalog of Inferred Sequence Binding Preferences, is an online library of transcription factors and their DNA binding motifs. Cis-BP is a collaboration between the labs of Tim Hughes (University of Toronto) and Matt Weirauch (Cincinnati Children's Hospital Medical Center).
- UCSC Arabidopsis Genome Browser Gateway
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The genome browser provides a gateway for visualizing the genome by position, gene or track type. The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group at the University of California Santa Cruz (UCSC).
- AGRIS
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The Arabidopsis Gene Regulatory Information Server (AGRIS) is an information resource of Arabidopsis promoter sequences, transcription factors, and their target genes. It houses databases of cis-regulatory elements, transcription factors, and transcription factor-target gene direct interactions. AGRIS was made by the Grotewold Lab at the Ohio State University.
- Araport
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The Arabidopsis Information Portal is a community resource for data mining the Arabidopsis thaliana genome to analyze gene structure, gene expression, protein function, and interaction networks, from the J. Ventor Institute, the University of Texas at Austin, and the University of Cambridge.
- Athena
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Athena is an Arabidopsis thaliana promoter database with visualization, data mining, and analysis tools from the laboratory of John Wyrick at Washington State University.
- BAR Bioinformatics
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The Bio-Analytic Resource for Plant Biology enables genomic expression and protein analysis. From the Provart Laboratory at the University of Toronto, Canada.
- Integrative Genomics Viewer
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The Integrative Genomics Viewer is a visualization tool from the BROAD Institute for interactive exploration of genomic data sets including Arabidopsis thaliana.
- Grassius
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GRASSIUS provides a public web resource composed of a collection of databases, computational resources, and experimental resources that relate to the control of gene expression in the grasses. From the Grotewold Laboratory at the Ohio State University and the Gray Laboratory at the University of Toledo.
- EnsemblPlants
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EnsemblPlants is a genome browser for genomic assembly, genomic annotatation, and comparative genomics resource from the European Bioinformatics Institute and the Wellcome Trust Sanger Institute.
- SIGnal
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SIGnal is a functional genomics suite of tools for genomic, epigenomic, and transcriptomic analysis of Arabidopsis and other plants from the Salk Institute Genomic Analysis Laboratory, Dr. Joseph Ecker, Director. SIGnal also provides a portal to Salk Arabidopsis 1001 Genomes, a partner site to the 1001 Genomes joint project, providing access to the GEBrowser, genome browser, and a library of Arabidopsis strain and SNP sequence data.
- 1001 Genomes
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The 1001 Genomes Project is a joint project to discover the whole-genome sequence variation in 1001 strains of the reference plant Arabidopsis thaliana. To date, more than 1100 lines have been sequenced. A list of the joint data providers is available here.
- TAIR Tools
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TAIR Tools - Links to TAIR analysis and visualization tools. The Arabidopsis Information Resource is a genetic and molecular biology resource for Arabidopsis thaliana from the Arabidopsis Biological Resource Center at the Ohio State University.
- BLAST
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BLAST - Arabidopsis thaliana NCBI Basic Local Alignment Search Tool for sequence searching and alignment.
- VirtualPlant
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VirtualPlant integrates genomic data and provides tools for visualization and analysis from the Systems Biology perspective, from the Coruzzi and Shasha Laboratories of New York University and the Gutierrez Laboratory of the Pontificia Universidad Catolica de Chile.
- GenBank
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GenBank is the National Institutes of Health (NIH) genetic sequence database resource.