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 including versions 5.0 and 6.1. The sequence comes from the International Rice Genome Sequencing Project (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.

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