Spacedust: de novo discovery of conserved gene clusters. Combining sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes. 🚀📄1/6🧵

RT @biorxiv_bioinfo: UniOP: a universal operon prediction for high-throughput prokaryotic (meta-)genomic data using intergenic distance ht….

RT @biorxiv_bioinfo: De novo discovery of conserved gene clusters in microbial genomes with Spacedust #biorxiv_bio….

I presented Spacedust at the ISMB/ECCB 2023. The talk is available online:. This was a collaboration with @milot_mirdita and @SoedingL. Thanks for the feedback and advice from @thesteinegger, Hong Su and Eli Levy Karin. 6/6.

Spacedust is freely available at GitHub, static binary and soon Bioconda. We have a Google Colab notebook to explore conservation of genomes of interest in a reference database with just a single click. Please give it a try and help improve Spacedust! 5/6.

Spacedust recovers previously annotated gene clusters e.g. operons, antiviral defense systems, and BGCs. It also identifies several more instances of CRISPR subtype III-E in the GTDB. 4/6

We searched all-vs-all with 1308 bacterial genomes from different genera. 1) Spacedust assigns 58% of all 4.2M genes & 35% of the unannotated genes into conserved gene clusters. 2) It offers better functional association prediction based on the congruence of KEGG module IDs. 3/6

Spacedust finds all gene clusters significantly conserved between any two genomes in a set of input genomes, by maximizing the statistical significance of the degree of clustering and order/strand conservation, therefore being reference-free. 2/6

SpacePHARER phage-host prediction using CRISPR spacers is now available in Google Colab. Simply hit “Run all” and upload your spacer files or phage genomes when prompted to visualize the matched phage or host. Thanks to @milot_mirdita.Try it out here:

RT @simroux_virus: Working with phages from metagenomes, and hoping to predict their host(s) ? Or you may be curious about how the newest h….

RT @banskt: Happy to see our method for predicting trans-eQTLs published at @GenomeBiology. Demonstrated on #eQTL data from @GTExPortal. Fu….

RT @slmsoh: Super excited to share our thermodynamic model for de-novo discovery of bipartite motifs in RNA sequences. @SoedingL @mpi_bpc….

RT @SimonStitzinger: Super excited to share the @biorxivpreprint of my first ever paper! We demonstrate with a thermodynamic model, the dra….

Happy to present a poster at my very first conference #GI2020, on de novo prediction of phage-host relationships via CRISPR spacers using our tool SpacePHARER. Check out our poster: and the preprint: .

RT @HorizonsMolBio: It’s official! Registration for #Horizons2020 #HorizONline🌅 opens on 𝟭𝘀𝘁 𝗝𝘂𝗹𝘆 𝟮𝟬𝟮𝟬! 🎉. Participation is FREE for everyo….

RT @biorxivpreprint: SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts #bio….

SpacePHARER finds phage host pairs based on CRISPR spacers. We find 4 times more phage-host associations than BLASTN did, strictly control for false ones, and are >13x faster. 📃 💾 Available on Conda and Docker Hub.