UK CropNet databases: a brief guide

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UK CropNet databases a brief guide

• Keith Bradnam
• Nottingham Arabidopsis
• Stock Centre

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UK CropNet Databases
MilletGenes
Arabidopsis Genome Resource (AGR)
BarleyDB
FoggDB
BrassicaDB
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ACEDB

• A Caenorhabditis elegans Database
• Intititally developed for worm data
• Developed for biologists by biologists
• Available for all computer platforms

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Advantages of ACEDB

• It works!
• Configurable
• Under constant development
• Good feedback from creators
• Can access ACEDB databases via web
• Its free!

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Disadvantages of ACEDB

• Its free!
• No manual
• Not always intuitive to use

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ACEDB database structure

• Data arranged into categories called classes
• Data can be (almost) anything, e.g. Author,
  genetic map, sequence, picture etc.
• Data in any one class can be linked to data in
  others

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Example database
Database
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Searching ACEDB databases

• Basic text search
• Browse data by surfing
• Powerful query language
• Find Author May Follow Paper Follow Sequence
  Clone
• Many plugins available, e.g. BLAST search
  against sequences

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Local vs remote databases

• People want web access to databases
• Dont have space on their machine
• Dont have expertise
• Dont have time
• People familiar with the web
• Web based databases are not so powerful

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Xace screenshot 1
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UK Cropnet Screenshot 1
ukcrop.net/
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UK Cropnet Screenshot 2
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Acebrowser Screenshot 1
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EcoSys
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AGR a complex ACEDB database

• There is a lot of Arabidopsis information
  available!
• 130 Mb genome, nearly completed
• Both major ecotypes have been sequenced
• Organising so much data is not easy!
• Why is there so much data?

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Smallest plant genome?
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What data is in AGR?

• Sequences (updated daily)
• AGI genome sequence (1,500 clones)
• EST and GSS sequences
• Organelle sequences
• Other ecotype sequences
• Protein sequences (Swissprot TREMBL)
• Insert sequences
• 225,000 sequences in total

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Other AGR data

• Maps and markers
• Physical, genetic, and recombinant inbred (RI)
  maps
• 1,200 RI markers
• RI scoring information
• Clone, Locus, and Allele info
• Germplasm info with links to order stocks

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Still more AGR data

• Bibliographic data (from EMBL records)
• Images (plants and gels)
• Other species info (protein sequences and
  associated info from all higher plant species)
• BLAST homologies millions of hits
• Mostly intra-specific homologies
• Some inter-specific homologies

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Acebrowser Screenshot 2
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Acebrowser screenshot 3
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AGR page screenshot
ukcrop.net/agr/
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AGR page screenshot2
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Insert lines

• Many Arabidopsis plants now contain random
  transposon insertions
• Therefore genes of interest may be hit, or
  modified by inserts
• Genomic location of inserts identified by blast
  analysis
• Can only identify putative location

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Insert data in AGR

• SINS (Jones) inserts
• Stocks sequences
• IMA (Sundaresan) inserts
• Stocks some location info
• ITS (Pereira) inserts
• Just sequences
• Separate web page for inserts
• ukcrop.net/agr/insert.html

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Xace screenshot
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Webace screenshot
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Searching for inserts
Find sequence of interest in AGR
Look to see if sequence has homology to an insert
BLAST search your sequence against insert
sequences
Search against precomputed BLAST analysis
Look to see if corresponding stocks are available
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NASC blast server
nasc.nott.ac.uk/blast.html
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Search precomputed blast data
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Future developments

• More data
• Microarray data
• More insert sequences
• Improved access to data
• New look to Acebrowser interface
• Bring GFace interface online
• More links between NASC and AGR