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VIGS-Mediated Forward Genetics Screening for Identification of Genes Involved in Nonhost Resistance
Published on: August 23, 2013
NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction
Sandeep K Kushwaha1, Pallavi Chauhan2, Katarina Hedlund2
1Department of Biology, Lund University, Ecology Building, Lund 22363, Sweden, PlantLink, Department of Plant Protection, Swedish University of Agricultural Sciences, Alnarp, Sweden and Bioinformatics Infrastructure for Life Sciences (BILS), Lund University, Lund, Sweden.
Unlabelled:
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.
Availability And Implementation:
The NBSPred pipeline is available at http://soilecology.biol.lu.se/nbs/
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Contact:
sandeep.kushwaha@biol.lu.se.
