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Arabimarklet: Tools to Jump across Arabidopsis Databases

Arabimarklets are easy-to-use JavaScript Bookmarklets for plant researchers.
When you are at ANY website that contains At0g00000-type gene codes, Arabimarklets can immediately bring you to the corresponding entries at your favorite databases.

How to Use: (Japanese introduction by Dr. Obayashi is available at Nazuna ML Log)

1. Right-click a To ... link to your favorite website and select "Add to Favorites" (Internet Explorer) or "Bookmark this link" (Firefox) to bookmark it. If you use Safari or Chrome, please drag-and-drop the link to the bookmark bar.

2. Visit ANY website that contains Arabidopsis gene IDs.

3. Open that bookmark! (You may need to allow pop-up windows.)

If you wish to test how these Arabimarklets work...

Just please left-click the To ... links.
They will automatically find gene ID(s) in the page content (see 4 lines above!) and immediately bring you to the corresponding entry in the selected database.
Arabimarklets do the same wherever you are.

Arabimarklet Showcase

 To TAIR

Comprehensive Arabidopsis information resource.

 To AtGDB

Sequence-centered genome view, with a narrow focus on gene structure annotation.

 To AtGenExpress

Microarray data and sample descriptions from the AtGenExpress project.

 To Athamap

Genome-wide map of potential transcription factor and small RNA binding sites.

 To AtProteome

Proteome database with a proteogenomic mapping of the peptides onto the genome.

 To ATTED-II

Gene coexpression database (Arabidopsis Thaliana Trans-factor and cis-Element prediction Database).

 To e-FP

Website for exploring microarray and other data for hypothesis generation (Electronic fluorescent pictographic browser). Part of Bio-Array Resource for Plant Functional Genomics (BAR).

 To Gclust

Databases of homologous proteins, automatically constructed but from a biologist's viewpoint.

 To Genevestigator

A user-friendly expression visualization tool, bringing gene expression into the context of thousands of conditions.

 To GO

Gene Ontology database.

 To InParanoid

Eukaryotic ortholog group database.

 To KATANA

Kazusa Arabidopsis thaliana Annotation Abstract, containing information and annotations of genes and proteins, gene families, gene ontology terms, metabolic pathways and gene expression data.

 To KEGG

Kyoto Encyclopedia of Genes and Genomes.

 To MAtDB

Comprehensive Arabidopsis thaliana Database at MIPS (Munich Information Center for Protein Sequences).

 To MPSS

MPSS (Massively parallel signature sequencing) mRNA tags (DpnII) and MPSS/454 small RNA data at University of Delaware.

 To NASCArrays Digital Northern

 To NASCArrays Spot History

Tools showing how genes are expressed over all the experiments in the Nottingham Arabidopsis Stock Centre's microarray database.

 To NCBI Gene

Gene database at NCBI.

 To NCBI AceView

A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences.

 To PGDD

Plant Genome Duplication Database, to identify and catalog plant genes in terms of intragenome or cross-genome syntenic relationships.

 To Phytozome

Database of clusters of orthologous and paraloous genes.

 To PlantCyc

A comprehensive plant biochemical pathway database.

 To Plaza

Comparative genomics resource to study gene and genome evolution in plants.

 To PPDB

Plant Proteome DataBase, storing experimental data from in-house proteome and mass spectrometry analysis, curated information about protein function, protein properties and subcellular localization.

 To RTSF Microarray Viewer

Arabidopsis developmental microarray data from the AtGenExpress Consortium, at Research Technology Support Facility, Michigan State University.

 To SALAD

Proteome database, containing protein motif structure and phylogenetic information.

 To Salk SNP Viewer

Arabidopsis SNP Sequence Viewer at Salk Institute.

 To SBS

SBS (Sequencing By Synthesis) mRNA tags (DpnII) and MPSS/454 small RNA data at University of Delaware.

 To StarNet2

A visual data mining front end for exploring correlation networks constructed from microarray data.

 To SUBA

SubCellular Proteomic Database, housing large scale proteomic and GFP localisation sets from cellular compartments of Arabidopsis.

 To T-DNA Express

Arabidopsis Gene Mapping Tool at Salk Institute.

 To TileViz

Tiling array data with ATH1 array data.

Inquiries

Please email iwasaki@k.u-tokyo.ac.jp (Wataru IWASAKI) or tweet to me in English or Japanese if you need bookmarklets to other databases or found any problems regarding these tools.
They do not do anything other than opening new browser windows, and have no security risks.
Arabimarklets do not work on Internet Explorer 6.

History

[Sep 28 2010] Address corrected: To AtGDB
[Sep 23 2010] Database added: To StarNet2
[Sep 16 2010] Version 3.1 released: Performance improved.
[Sep 12 2010] Version 3.0 released: now Arabimarklets can handle cases that more than 6 gene IDs are found.
[Sep 9 2010] Databases added: To Genevestigator, To NCBI Gene, To NCBI AceView, To PGDD, To PlantCyc, and To PPDB
[Sep 9 2010] Version 2.2 released: now Arabimarklets convert gene IDs to the At*g***** case style.
[Sep 8 2010] Version 2.1 released: now Arabimarklets open up to 5 windows even if more IDs are found.
[Sep 7 2010] Version 2.0 released: now Arabimarklets (1) search page content if URLs do not contain Gene IDs and (2) open multiple windows if multiple IDs are found.
[Sep 7 2010] Database added: To Gclust
[Sep 6 2010] Databases added: To GO and To KEGG
[Sep 4 2010] Version 1.0 released.