UniHH

Peroxisome Biology of Plants and Microalgae

Research group by Prof. Dr. S. Reumann
Centre for Organelle Research (CORE)
University of Stavanger, Norway		 UiS logo
Arabidopsis and Microalgae

  • About us
    • Welcome
    • Contact
  • Research
    • Overview
    • Research projects
      • Bioinformatics
      • Innate immunity
      • Microalgae research
      • Proteomics
      • Stress adaptation
  • Publications
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    • alphabetical
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  • Group members
    • Overview
    • A. Benichou
    • M. Budathoki
    • S. Charlesworth
    • Dr. G. Chowdhary
    • D. Crappe
    • M. Deus
    • E. Drange Vee
    • D. Kechasov
    • P. Lisik
    • S. Reumann
    • A. Sharma
    • Dr. K. Sorhagen
    • S. Werner
    • Bachelor students
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    • UiS links
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    • Prekubator AS
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Research projects: Reumann lab > Research projects > Bioinformatics
Bioinformatics
Innate immunity
Microalgae research
Proteomics
Stress adaptation


TL
Dr. Thomas Lingner
(Goettingen, Germany)


PredPlantPTS1
Prediction server "PredPlantPTS1"


AraPerox
Database "AraPerox"

Computational prediction of peroxisomal proteins and
organelle functions from genome sequences


In a computational approach, which is complementory to experimental proteome research, we are developing algorithms to predict matrix proteins of plant peroxisomes with high accuracy from genome sequences. This research is carried out in tight and most fruitful collaboration with Dr. Thomas Lingner (University of Goettingen, Germany). We applied discriminative machine learning methods to predict the major class of peroxisomal matrix proteins carrying peroxisome targeting signals type 1 (PTS1) from genome sequences. Experimental validation of the predictions by in vivo subcellular targeting analysis demonstrated a high prediction accuracy (Lingner et al., 2011; Chowdhary et al., 2012). The prediction tool has been made publicly available to the scientific community via the public Web server "PredPlantPTS1" (ppp.gobics.de; Reumann et al., 2012).
The prediction of plant PTS2 proteins is in progress. Arabidopsis proteins predicted to be targeted to peroxisomes have been assembled in the database AraPerox 1.2 (www3.uis.no/araperoxv1/). A new relational format of the database is currently being developed.






PWM
PTS1 protein predictions for Arabidopsis
thaliana by two different models
 Pex5p
Pex5p receptor for PTS1 proteins






PTS1
Plant PTS1 tripeptide motif