Katarina Hedlund
Professor
NBSPred: A support vector machine-based high throughput pipeline for plant resistance protein NBSLRR prediction.
Author
Summary, in English
The nucleotide binding site-leucine-rich repeats (NBSLRR) belong to one of the largest known families of disease resistance genes that encode resistance proteins (R-protein) against the pathogens of plants. Various defence mechanisms have explained the regulation of plant immunity, but still, we have limited understanding about plant defence against different pathogens. Identification of R-proteins and proteins having R-protein-like features across the genome, transcriptome and proteome would be highly useful to develop the global understanding of plant defence mechanisms, but it is laborious and time consuming task. Therefore, we have developed a support vector machine (SVM) based high throughput pipeline called NBSPred to differentiate NBSLRR and NBSLRR-like protein from Non-NBSLRR proteins from genome, transcriptome and protein sequences. The pipeline was tested and validated with input sequences from 3 dicot and 2 monocot plants including Arabidopsis thaliana, Boechera stricta, Brachypodium distachyon Solanum lycopersicum and Zea mays.
Department/s
- Biodiversity
- Evolutionary ecology
- Soil Ecology
Publishing year
2015-12-09
Language
English
Pages
1223-1225
Publication/Series
Bioinformatics
Volume
32
Issue
8
Document type
Journal article
Publisher
Oxford University Press
Topic
- Bioinformatics (Computational Biology)
Status
Published
Research group
- Soil Ecology
ISBN/ISSN/Other
- ISSN: 1367-4803