Our code is maintained at Krasileva Lab GitHub.
Available under MIT license.
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.
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
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.
Identification of neighboring genes, used in Bailey et al. Genome Biology 2018. Developed by Christian Schudoma.
anchoring to genetic map code here
circos plot visualization code here
Extracting leucine Rich Repeat Motifs with regular expression. Currently, under development by Ksenia,
Our code is probably not going to help you at the moment, but if you need to predict LRRs, this is the best published software that we have tested (not written by us): LRRpredictor (web server link, GitHub link)
Phylogenetics tutorial with NLR-ID examples
Graduate module in Genomic and Bioinformatics (for general plant biologists)
2020 Lecture notes (developed by Ksenia, taught without ppt):
- Phylogenomics tutorial (updated version): Workshop1_Tutorial_Phylogenomics_PMB200B_v2 with introductory slides: Workshop1_introduction_2021
- NGS analyses with Galaxy (compilation): Workshop2_Tutorial_NGS_PMB200B