AGR

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AGR

• What is AGR?
• AGR is an abbreviation of Arabidopsis Genome
  Resource.
• What is inside?
• 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

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• 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
  
• Insert data - details of insert sequences and
  their genomic locations
• Images - pictures of plants and DNA gels
• BLAST homology information (millions of
  individual BLAST hits)

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3. Where the data come from?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).

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4. What is ACE_DB ?

• AceDB was originally developed for the C.elegans
  genome project , from which its name was derived
  (A C. elegans DataBase).

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5. How the ACEDB works?

• 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.

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• 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

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6. About Maps

• As we mentioned above, there are mainly two type
  of maps in the ACE_DB
• Genetic map
• Physical map

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An Acedb sequence imasge
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A physical map
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One more graphycal dispay
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7. How Blast against AGR?

• The sequences have been BLAST searched against
  the proteins in AGR. So a user can find a gene of
  interest in their favourite species, and then see
  (and navigate to) what the most likely homologue
  in Arabidopsis is.

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8. How it works ?
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