NBSPred：一种基于支持向量机的高通量植物抗病蛋白 NBSLRR 预测流水线。

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

机构信息

Department 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.

Department of Biology, Lund University, Ecology Building, Lund 22363, Sweden.

出版信息

Bioinformatics. 2016 Apr 15;32(8):1223-5. doi: 10.1093/bioinformatics/btv714. Epub 2015 Dec 9.

DOI:10.1093/bioinformatics/btv714

PMID:26656003

Abstract

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.

摘要

未加标签

核苷酸结合位点富含亮氨酸重复序列（NBSLRRs）属于已知最大的疾病抗性基因家族之一，该基因家族可编码植物抗病原体的抗性蛋白（R 蛋白）。各种防御机制解释了植物免疫的调控，但我们对植物抵御不同病原体的防御仍知之甚少。跨基因组、转录组和蛋白质组鉴定 R 蛋白和具有 R 蛋白样特征的蛋白质，对于发展对植物防御机制的全面理解将非常有用，但这是一项费力且耗时的任务。因此，我们开发了一种基于支持向量机的高通量管道，称为 NBSPred，用于从基因组、转录组和蛋白质序列中将 NBSLRR 和 NBSLRR 样蛋白与非 NBSLRR 蛋白区分开来。该管道已通过来自三种双子叶植物和两种单子叶植物的输入序列进行了测试和验证，包括拟南芥、Boechera stricta、Brachypodium distachyon、番茄和玉米。