The purpose of this repository is to help you find where your NLR sequence fits in the pan-NLRome of your species of interest.
Currently NLRCladeFinder supports Maize, Arabidopsis, and Soy NLRs.
To open the Colab notebook, click the file NLRCladeFinder.ipynb and then click "Open in Colab" button at the top of the file.
This will create a copy of the notebook where you can input your sequence of interest and also modify the code as you like.
Video walk through of the NLRCladeFinder is in the NLRCladeFinder_Tutorial.mp4 file. Instructions for vieiwing entropy annotations in Chimera are in the ViewingInChimera_Tutorial.mp4 file.
If you find this useful, please cite our preprint and the relevant pan-NLRome source.
Majority of the highly variable NLRs in maize share genomic location and contain additional target-binding domains Daniil M. Prigozhin, Chandler A. Sutherland, Sanjay Rangavajjhala, Ksenia V. Krasileva bioRxiv 2022.10.05.510735; doi: https://doi.org/10.1101/2022.10.05.510735
Arabidospsis:
Van de Weyer, A.-L. et al. (2019). A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell 178: 1260–1272.e14.
Maize:
Hufford, M.B. et al. (2021). De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373: 655–662.
Soy:
Liu, Y. et al. (2020). Pan-Genome of Wild and Cultivated Soybeans. Cell 182: 162–176.e13.
Also consider citing our hvNLR paper.
Prigozhin, D.M. and Krasileva, K.V. (2021). Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites. Plant Cell 33: 998–1015.