Toolbox

Code

Our code is maintained at Krasileva Lab GitHub.

Available under MIT license.

Protein family analyses

  • Plant R-genes: Scripts to annotate Pfam domains, extract NLR plant immune receptors and their architectures, including NLR-ID, 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. (link to the code)
  • Tandem: Identification of neighboring genes, used in Bailey et al. Genome Biology 2018. Developed by Christian Schudoma. (link to the code)
  • ASTREL_NLR: Scripts and supplemental files used in Baggs et al 2020 to perform identification of orthogroups lost together with NLRs and EDS1 signaling pathway.  (link to the code)
  • hvNLRs: Scripts used in Prigozhin and Krasileva 2021 to phylogenetically group NLRs from pan-genomes into allelic series, perform Shannon Entropy analyses and predict ligand binding sites: (link to the code)

Plant genomics and variant discovery

Teaching Materials

Graduate module in Genomic and Bioinformatics (for general plant biologists)

2020 Lecture notes (developed by Ksenia, taught without ppt):

  1. Gene families
  2. Genomic diversity
  3. Functional genomics
  4. Beyond a typical genome
  5. Emerging topics

Workshops and tutorials

  1. Phylogenomics tutorial (Google docs, link) with introductory slides: (ppt, link)
  2. NGS analyses with Galaxy (compilation): (Word doc, link)
  3. Genome annotation tutorial (Google colab, link)