ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB imports model DNA sequences (pseudomolecules/exons) from Michigan State University’s Rice Genome Annotation Project (MSU RGAP http://rice.plantbiology.msu.edu/) including versions 5.0, 6.0, 6.1 and 7.0. 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
  • N/A.
  • Flat file info pages show model DNA sequences from MSU.
Example: find DNA sequence for LOC_Os07g18120.1
There are 78 sequences with N's.
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Nucleotide Code & Wildcards

http://www.ncbi.nlm.nih.gov/staff/tao/tools/tool_lettercode.html

Code Base
Aadenine
Ccytosine
Gguanine
Tthymine
Wildcard Description Bases
NanyACGT
Bnot ACGT
Dnot CAGT
Hnot GACT
Vnot TACG
Wildcard Description Bases
WweakAT
SstrongCG
RpurineAG
YpyrimidineCT
MaminoAC
KketoGT

System Information

Transcript of last update

Took 19 minutes, 29 seconds, 538 millis starting Thu, 19 Apr 2012 14:03:57 GMT:
Using /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/TIGRDNA_
Using db.local/downloaded/TIGRDNA_
Importing all.5.seq
Importing all.6.seq
Importing all.7.seq