Toolbox

Code

Our code is maintained at Krasileva Lab GitHub.

Available under MIT license.

Plant R-genes

code here

Scripts to annotate Pfam domains and extract NLR plant immune receptors and their architectures as published in Sarris et al BMC Biology 2016. Originally, written by Ksenia, now updated and maintained by the group, including contributions from Erin Baggs.

SCVEP

code here

Annotation-free variant effect prediction. It is based on blasting DNA sequence surrounding the SNP against protein database and resulting alignment is used to predict likely effect of the SNP on the coding sequence. Developed by Christian Schudoma.

Wheat TILLING PNAS 2017

code here

Collaborative set of scripts used in Krasileva et al 2017 Wheat TILLING publication. Forked from repository. Contributions from Hans Vasquez-Gross, Ricardo Ramirez-Gonzalez, Paul Bailey, Ksenia Krasileva, Christian Schudoma.

Tandem

code here

Identification of neighboring genes, used in Bailey et al. Genome Biology 2018. Developed by Christian Schudoma.

TGACv1-circos

anchoring to genetic map code here

circos plot visualization code here

Scripts we developed and used in Clavijo et al. 2017 to order genome scaffolds and to plot genetic map of wheat. Developed by Christian Schudoma.

LRR crawler

code (in development) here

Extracting leucine Rich Repeat Motifs with regular expression. Currently, under development by Ksenia,

Teaching Materials

Phylogenetics tutorial with NLR-ID examples

Link to Google Docs

Erin Baggs, Elisha Thynne and Ksenia Krasileva assembled the tutorial and taught this module during TSL Summer School in Plant-Microbe Interactions, 2017.