NBSPred: a support vector machine-based high throughput pipeline for plant resistance protein NBSLRR prediction

Abstract

The nucleotide binding site leucine-rich repeats (NBSLRRs) 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-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 three dicot and two monocot plants including Arabidopsis thaliana, Boechera stricta, Brachypodium distachyon Solanum lycopersicum and Zea mays.

Published in

Bioinformatics
2016, volume: 32, number: 8, pages: 1223-1225
Publisher: OXFORD UNIV PRESS

SLU Authors

• Kushwaha, Sandeep Kumar

  • Department of Plant Protection Biology, Swedish University of Agricultural Sciences
    
  • Lund University

Associated SLU-program

SLU Plant Protection Network

UKÄ Subject classification

Bioinformatics (Computational Biology)

Publication identifier

• DOI: https://doi.org/10.1093/bioinformatics/btv714

Permanent link to this page (URI)

https://res.slu.se/id/publ/83252