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NBSPred: A support ...
NBSPred: A support vector machine-based high throughput pipeline for plant resistance protein NBSLRR prediction.
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- Kushwaha, Sandeep (author)
- Sveriges lantbruksuniversitet,Swedish University of Agricultural Sciences,Lund University,Lunds universitet,Biodiversitet,Biologiska institutionen,Naturvetenskapliga fakulteten,Biodiversity,Department of Biology,Faculty of Science,Växtskyddsbiologi,Department of Plant Protection Biology
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- Chauhan, Pallavi (author)
- Lund University,Lunds universitet,Evolutionär ekologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Evolutionary ecology,Department of Biology,Faculty of Science
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- Hedlund, Katarina (author)
- Lund University,Lunds universitet,Biodiversitet,Biologiska institutionen,Naturvetenskapliga fakulteten,Biodiversity,Department of Biology,Faculty of Science
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- Ahrén, Dag (author)
- Lund University,Lunds universitet,Biodiversitet,Biologiska institutionen,Naturvetenskapliga fakulteten,Biodiversity,Department of Biology,Faculty of Science
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(creator_code:org_t)
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- 2015-12-09
- 2015
- English.
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:8, s. 1223-1225
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Publication and Content Type
- art (subject category)
- ref (subject category)
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