ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB imports model protein sequences 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 DNA 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 protein sequences from MSU.
Example: find peptide sequence for LOC_Os07g18120.1
There are 20 sequences with X's.
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The Code

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

A  alanine               P  proline
B  aspartate/asparagine  Q  glutamine
C  cystine               R  arginine
D  aspartate             S  serine
E  glutamate             T  threonine
F  phenylalanine         U  selenocysteine
G  glycine               V  valine
H  histidine             W  tryptophan
I  isoleucine            Y  tyrosine
K  lysine                Z  glutamate/glutamine
L  leucine               X  any
M  methionine            *  translation stop
N  asparagine            -  gap of indeterminate length

System Information

Transcript of last update

Took 3 minutes, 21 seconds, 659 millis starting Thu, 19 Apr 2012 14:00:15 GMT:
Using /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/TIGRPEP_
Using db.local/downloaded/TIGRPEP_
Importing all.5.pep
Importing all.6.pep
Importing all.7.pep