ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB imports dual-targeting scores from "ATP" — an ambiguous-targeting predictor and outputs the score as a percentage. Scores above 50% imply ambiguous targeting and can be searched in Rice DB as either mitochondrial or plastid. Scores at or below 50% have low likelihood of ambiguous targeting, but no conclusion is drawn about which specific location is targeted — these results are unsearchable. From their website:

“This SVM-tool tests whether the first 70 amino acids of a plant protein sequence are likely to encode an ambiguous mt/pt targeting signal. If so, the mature protein might be dually targeted to mitochondria and plastids. The score interval ranges from 0.0 to 1.0, the higher the score, the more reliable it is.”

Citations:

Mitschke J., Fuss J., Blum T., Hglund A., Reski R., Kohlbacher O., Rensing S.A. (2009): Prediction of dual protein targeting to plant organelles. New Phytol. epub Apr 7th

Usage When Searching Rice DB Usage Viewing Rice DB Results
  • Can search either for mitochondria or plastid in 'atp' for dual-targeted loci.
  • Dual-targeting scores are shown as percentages in 'atp' column.
Example: show ATP for LOC_Os02g07760.1
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System Information

Transcript of last update

Took 12 seconds, 763 millis starting Fri, 24 Aug 2012 04:02:18 GMT:
Using /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/AmbiguousTargetingPredictor_
Using db.local/downloaded/AmbiguousTargetingPredictor_
Using atp.csv Fri Aug 24 08:15:24 WST 2012
SQL data loaded
Location statistics summarised
Full-text index and stems updated