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 ~ Arabidopsis Genome Resource (AGR)

Quick search AGR... 
Type in a relevant keyword or phrase, e.g. 'auxin', 'RNA helicase', 'lax2', 'Bennett', 'homeobox protein'

AGR is a database developed at NASC using the ACEDB database system. Sequences, maps, and other information has been combined to form a large and powerful information resource. To start exploring AGR, use the search box above or select a link from below:

about AGR | accessing AGR | AGR help
AGR sequences | AGR maps | other AGR data


~ AGR news ~



The Final rebuild of the AGR Database - 20/03/03.
Please note: AGR is no longer being maintained. The final update of the database took place in March 2004.
Please visit Arabidopsis Ensembl - Arabidopsis.info's (NASC) new genomic resource.

More AGR news... Latest AGR version - 2.65


Accessing data in AGR
Although AGR can be
downloaded and installed on your own system, the easiest way to explore AGR is via the web. The data in AGR are conveniently organised into classes which can be browsed or searched. Explore the following links and drop-down menus to browse these classes.

Browse Arabidopsis sequences:

Notes on sequence displays
Sequences can be viewed as an image, as a comprehensive 'sequence report' or in the native database format ('tree display'). A 'sequence report' allows you to view your sequence in a simple format (either spliced, unspliced or translated) suitable for cutting and pasting into other applications (e.g. you can BLAST search against any of the databases on the UK CropNet server). Note that much BLAST analysis is pre-computed and stored within AGR.

  • Click here to see a guide to the AGR sequence display


  • Browse maps in AGR:

    Notes on maps
    There are currently three types of map for each of the five Arabidopsis chromosomes, and they are displayed using the same graphic display as for sequences. The Recombinant Inbred (RI) maps are curated here at NASC where other information about them is available.

  • Guide to map displays in AGR


  • Other Data Classes in AGR:

    Brief guide to other data classes

    • Author - Any author described in a database entry

    • Chromosome - Lists sequences associated with each chromosome

    • Clone - All Arabidopsis clones with links to sequences (if available)

    • AGI clone - Clones used in the Arabidopsis Genome Initiative (AGI)

    • IGF clone - Clones used to form the IGF BAC map

    • Gene name - Names taken from database entries

    • Gene product - Info. from coding sequence details in EMBL

    • Germplasm Resource - Details of available seed lines, linked to stock catalogue pages at NASC

    • Image - Images of germplasm resources and autorad gels

    • Journal - Information from database records

    • Locus - Information regarding sequences, clones, markers, probes, and genes

    • Paper - Information on papers from database records

    • Patent - Information on patented sequences from database records

    • Probe - Details of probes

    • Species - Sequences (DNA and Protein) of over 2,000 species are stored in AGR

  • Click here to go the AGR class browser to see all classes


  • Query AGR:

    Using the AGR query language
    The most powerful way to search AGR is by using the ACEDB query language. The examples in the drop-down menu above illustrate some of the types of queries that you can perform with this query language, though you can of course construct your own query. We hope to expand this section to provide a large range of pre-defined queries to retrieve very complex data from the database. If there is data that you would like to retrieve from AGR, then email us and we will try to construct a query that will help you. Any query constructed in this manner will then be added to the above list. We hope to return your query within a few hours.


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    ~ About AGR ~

    (Russian translation here thanks to Martha Ruszkowski)

    This section is intended to briefly explain a little about AGR, what is in it, and how you can download the database for local use. A more complete description of what is in AGR is available from the AGR help pages. These help pages are stored within AGR itself, and they also provide other information that is not covered on this page.

    What's in AGR?
    AGR contains several million pieces of data, most of which are cross linked to each other. The majority of this data consists of the following:

    • Sequences (DNA, RNA, and protein)
    • Maps and markers (Physical, Genetic, and Recombinant inbred maps)
    • Clone information for nearly 150,000 clones
    • Germplasm resources (details of over 10,000 stocks)
    • Authors, published papers, and patent information
    • BLAST homology information (millions of individual BLAST hits)
    • Insert data - details of insert sequences and their genomic locations
    • Images - pictures of plants and DNA gels

    DNA sequence information is updated daily from the EMBL database and protein sequence is updated regularly from the SwissProt and TREMBL databases to ensure that AGR contains all of the available Arabidopsis sequences. BLAST information is updated with each new release of EMBL (every 3 months).

    The ACEDB database system makes it easy for links to be generated between these different types of data. Each major category of data is known as a 'class' in ACEDB, and categories can also have subcategories, e.g. AGI_Genome_Sequence is a subcategory of the Sequence class and contains only those sequences that have been associated with the Arabidopsis genome project. Many of these classes are extremely large and not always easy to browse because there is so much data. The advantages of this database structure though is that the ACEDB query language can be used to extract very specific pieces of information. E.g. consider the following query:

    Find AGI_Genome_Sequence; Chromosome = "IV"; Follow Locus; Map 

    The semi-colons break up the individual parts of this query. In 'English' it reads as "Find all Arabidopsis genome sequences that are known to be on chromosome IV. Extract a list of all loci objects from this, and only list those which are known to have a map position.". This query returns a list of about 150 loci objects, all of which have a map position and also which correspond to a genome sequence from chromosome IV. This may not be what you are after, but it demonstrates how very specific queries can be made.

    Download AGR
    AGR is freely available for download from our
    FTP site. To use AGR in this way, you will also need to download an ACEDB executable from the Sanger Centre ACEDB site. ACEDB can be installed on UNIX, LINUX, Mac, and PC platforms. Once you have copied and installed your ACEDB program, copy the files from the above FTP link to a suitable location on your computer. You may wish to use a program such as Mirrorto do this.

    The minimum number of files that you need to copy are those that are in the /AGR/database folder on our FTP site. These represent the raw data files that comprise all of the information in AGR. However, you will probably also want to copy the images in the /AGR/externalFiles folder. Furthermore, if you want your copy of AGR to perfectly resemble the copy here, you will also need to copy the files in the /AGR/wspec folder. We therefore suggest that you simply copy the entire /AGR folder. Information on our FTP site is updated every night.

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    Help with using AGR
    If you are having a specific problem in using AGR, then feel free to
    email us and we will try to help you with any difficulties you are having. If you want to know more about how the ACEDB database system works then try reading this guide at the Sanger Centre or look at the AGR help pages. You may wish to try both of the available web interfaces to AGR. All other links on this page enter AGR using the AceBrowser interface. WebAce allows for more flexibility when viewing images (you can scroll and resize images).

    Arabidopsis Genome Resource maintained by:
    David J Craigon
    Graeme Gill
    Guo An Sun
    Sean May (Principal Investigator)

    Plant Science Division, Sutton Bonington Campus,
    University of Nottingham,
    Loughborough,
    LE12 5RD, UK




     ~ Links

    NASC
    Nottingham Arabidopsis Stock Centre

    InsertWatch
    New from NASC: let NASC 'watch out' for inserts that may match your gene of interest

    NASC BLAST server
    For searching against insert sequences

    Simple AGR search
    An easier, more helpful, way to search AGR

    AGR insert page
    Detailed info. about insert sequences in AGR

    GARNet
    Genomic Arabidopsis Resource Network

    MATDB
    MIPS Arabidopsis thaliana database

    TAIR
    The Arabidopsis Information Resource

    AGAD
    Arabidopsis Gene Annotation Database - at TIGR

    NCBI Arabidopis page
    Part of the excellent NCBI's Genome site

    DATA
    Database of Arabidopsis thaliana annotation

    GABI Arabidopsis page
    GABI is the German plant functional genomics project

    Génoplante
    The French functional genomics project

    KAOS
    Kazusa Arabidopsis Opening site

    Search KEGG
    Kyoto Encyclopedia of Genes and Genomes

    AtRepBase
    Database of Arabidopsis repeat sequences

    Newsgroup
    Access recent postings to the arabidopsis newsgroup

    Nature Genome Gateway
    A comprehensive genomics web site

    Other Arabidopsis sites
    Arabidopsis links at the Google search directory

    BBSRC grants
    List current Arabidopsis-related BBSRC grants


    Contact us
    Please email us if you have any questions.



    Page last modified: Thursday, 02-May-2013 11:03:04 BST
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