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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http//ukcrop.net
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Where are we?
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UK CropNet Databases
MilletGenes
Arabidopsis Genome Resource (AGR)
BarleyDB
FoggDB
BrassicaDB
26 Other plant related databases
ukcrop.net/db.html
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BLAST server available

• Blast databases updated nightly
• Fast!
• ukcrop.net/perl/ace/ncbi_blast
• Blast server available from any database

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UK CropNet database usage
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Hits to UK CropNet website 1996-2000
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Where in the world?
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UK CropNet next year

• More databases? Have approached
• CompositDB
• LupinDB
• ZmDB
• SnapDragonDB
• PopulusDB
• GFace access
• ARCADE
• ComapDB

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Feedback

• If you like our databasestell us
• If you dont like our databasestell us!
• These databases are often easy to customise
• We are your loyal servants!!!

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Arabidopsis Genome Resource

• http//ukcrop.net/agr

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AGR a complex ACEDB database

• There is a lot of Arabidopsis information
  available!
• 130 Mb genome, essentially complete
• 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
• 230,000 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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AGR recent improvements

• More data
• e.g. EMBL sequences, protein sequences
• More annotation of existing EMBL data, e.g.
• Tissue type information
• Ecotype info
• CDS evidence
• Inclusion of new (non-EMBL) data, e.g.
• Insert sequences
• SNP data

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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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Its a knock-out!
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Its a knock-out!
ATCGCTTAAGGACTGGCACCAC
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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
• Launchpad (Muskett)
• Just sequences

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Finding an insert in your gene

• AGR and NASC provide many different ways of
  finding insert information
• ukcrop.net/agr/insert.html
• arabidopsis.org.uk/catalogue.html
• arabidopsis.org.uk/blast.html
• arabidopsis.org.uk/insertwatch

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Webace screenshot

• 1) find gene on interest in AGR

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Search precomputed blast data
2) search pre-computed blast analysis
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NASC blast server
3) blast search against insert database
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4) Register your sequences with InsertWatch
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Spreading the word

• Raise general awareness of AGR
• Many bioinformatics sites link to TAIR but not
  AGR
• Make people aware of AGR contents
• Sequences maps stocks papers etc.
• AGR vs TAIR
• AGR is now a lot faster for general queries
• No limits (as yet) on blast searching
• AGR contains the sequences
• AGR (hopefully) keeps things simple

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Future developments

• More data!
• Microarray data
• More insert sequences
• More links between NASC and AGR
• Acknowledgements Jamie Kincaid, NASC, UK CropNet

ukcrop.net/agr arabidopsis.org.uk/insertwatch