Projects per year
Abstract
There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provide focus for the more costly and time consuming functional assays that follow. DNA-binding proteins are an important class of proteins that require annotation, but current computational methods are not applicable for genome wide predictions in plant species. Here, we explore the use of species and lineage specific models for the prediction of DNA-binding proteins in plants. We show that a species specific support vector machine model based on Arabidopsis sequence data is more accurate (accuracy 81%) than a generic model (74%), and based on this we develop a plant specific model for predicting DNA-binding proteins. We apply this model to the tomato proteome and demonstrate its ability to perform accurate high-throughput prediction of DNA-binding proteins. In doing so, we have annotated 36 currently uncharacterised proteins by assigning a putative DNA-binding function. Our model is publically available and we propose it be used in combination with existing tools to help increase annotation levels of DNA-binding proteins encoded in plant genomes.
Original language | English |
---|---|
Article number | gvk805 |
Number of pages | 11 |
Journal | Nucleic Acids Research |
Volume | 43 |
Issue number | 22 |
Early online date | 24 Aug 2015 |
DOIs | |
Publication status | Published - 15 Dec 2015 |
Fingerprint
Dive into the research topics of 'DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool'. Together they form a unique fingerprint.Projects
- 2 Finished
-
RETRaIN: Rewiring the Nucleus Towards Plant Immunity
Huitema, E. (Investigator)
COMMISSION OF THE EUROPEAN COMMUNITIES
1/01/13 → 31/12/17
Project: Research
-
Strategic Award: Wellcome Trust Technology Platform
Blow, J. (Investigator), Lamond, A. (Investigator) & Owen-Hughes, T. (Investigator)
1/01/13 → 30/09/18
Project: Research