Project Hail Mary

DNAzyme-like motifs, horizontal gene transfer, and short linear motif conservation in Potyviridae

This repository is a reproducible research compendium documenting the discovery of a DNAzyme-like catalytic domain sequence conserved across several potyvirus species, with flanking regions matching eukaryotic genes across plant, fungal, and animal genomes — suggestive of cross-kingdom horizontal gene transfer. It also characterises a conserved motif in the potyviral CI (cylindrical inclusion) helicase implicated in host-sorting and immune-trafficking interactions (potentially via the AP-4 adaptor complex).

This is a preprint / work in progress and has not been peer reviewed. Several of the central ideas are presented as explicit, testable hypotheses rather than established results. See the book's preprint notice for the full caveat.

Structure

Path	Contents
notebooks/	The book's chapters (Quarto .qmd), numbered to match their rendered order
packages/potytools/	An R package of the reusable, tested analysis functions used across chapters — GenBank parsing, codon usage bias (RSCU/ENC/CAI), phylogenetics, sequence logos, host classification, motif-flank extraction. Being prepared for rOpenSci peer review
scripts/	One-off orchestration/data-preparation scripts (fetch external data, build an offline fallback tree, etc.) — run occasionally to regenerate a data/ artifact, not a function library
shiny/bionexus/	A companion Shiny app for live GBIF + GLOBI host–vector network exploration
data/	Sequence data, alignments, and cached lookups (not tracked in git; regenerate via the pipeline below)
_targets.R	The targets pipeline orchestrating the computationally intensive steps (alignment, phylogenetic inference, NCBI/ELM fetching)

Reading the book

The rendered book isn't currently published (see Status below). To read it locally:

install.packages(c("quarto"))
quarto::quarto_render()  # or: quarto render, from a terminal

Reproducing the analysis

# Install the pipeline dependencies once
install.packages(c("targets", "tarchetypes"))
remotes::install_local("packages/potytools")

# Run the full pipeline (skips up-to-date steps automatically)
targets::tar_make()

External tools required on PATH for the full pipeline: mafft, iqtree2, hmmscan. Package dependencies are pinned via renv; run renv::restore() to install the exact versions used.

potytools

Analysis functions are collected in the potytools R package (packages/potytools/), which is rOpenSci-standards-compliant (documented, tested, CI-checked) and being prepared for rOpenSci peer review.

remotes::install_local("packages/potytools")
library(potytools)

Status

• Book: actively evolving; content and interpretations may change between renders.
• potytools: tests passing, R CMD check clean, not yet submitted for review.
• Not yet published to GitHub Pages.

License

Code in packages/potytools/ is MIT-licensed (see packages/potytools/LICENSE). Sequence data and other third-party inputs under data/ retain their original source licensing/terms — see the data-sources appendix for provenance.