BRAKER4 is about to hatch. It now also covers functional annotation for protein sequences... #genomeannotation

This article is now published! academic.oup.com/nargab/artic...
We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

Release v1.1.7 · Gaius-Augustus/Tiberius ⚠️ New Models available: Diatoms Eudicotyledons Lepidoptera Monocotyledonae Mucoromycota Saccharomycota Sordariomycota Several bugfixes.

With help of international colleagues at @jgi.doe.gov, @oregonstate.edu, and @stockholm-uni.bsky.social, we are relasing new parameters for Tiberius. Thx to Lars Gabriel, @tomasbruna.bsky.social, Samuel Talbot, @chriswheat.bsky.social, @masta.bsky.social - and many others. github.com/Gaius-August...

Big thanks to @axelvisel.bsky.social for sharing! For full consideration, please apply by September 2.

pangenome 'expansion' curves for cotton and soybean

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.

We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...