ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB imports 1kb upstream DNA sequences from Michigan State University’s Rice Genome Annotation Project (MSU RGAP http://rice.plantbiology.msu.edu/) including versions 5.0 and 6.1. The sequence comes from the International Rice Genome Sequencing Project (IRGSP http://rgp.dna.affrc.go.jp/IRGSP/), Oryza sativa ssp. japonica cultivar Nipponbare.

Usage When Searching Rice DB Usage Viewing Rice DB Results
  • DNA oligomers (e.g., hexamers) can be searched for.
  • First 1000 upstream nucleotide bases are searched.
  • The minimum n-gram motif length is n=6.
  • Wildcards are understood for DNA sequences.
  • Flat file info pages show 1kb upstream DNA sequences from MSU.
  • 1kb upstream can be down in search results.
  • Hexamers can be shown in search results, with genome frequency rates.
Example: find 1kb upstream for LOC_Os02g06480.1
Example: view 1kb upstream for LOC_Os07g18120.1
Example: count TIGR IDs with ATCGAC
Example: find matching fields, annotations, predicted locations relating to ATCGAC
Example: atcgac
Example: atcgacat in 1kb upstream
Example: show hexamers for LOC_Os07g18120.1
Example: find hexamer motif frequencies relating to "map kinase"
Example: view hexamer counts matching "map kinase"
There are 105 sequences with N's.
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System Information

Transcript of last update

Took 28 minutes, 35 seconds, 612 millis starting Thu, 14 Jun 2012 02:50:35 GMT:
Using /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/TIGR1kb_
Using db.local/downloaded/TIGR1kb_
Calculating trimers for 68982 sequences
TIGR1kb indexing probe names
TIGR1kb indexing probe positions
Updating full text index