Joseph GuhlinGuide: Switching from Conda/Mamba to Pixi. Near instant environments, better HPC compatibility and reproducibility. But really, it's the speed!
Antonio Camargo
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Likes bioinformatics stuff
Marco MolariHappy to announce a new preprint from the lab, together with fantastic @richardneher and Liam Shaw! 📝
https://www.biorxiv.org/content/10.1101/2024.07.08.602537v1
We were motivated by the following puzzling observation: microbial genomes can be extremely similar in the core genome, while still differing by large portions of accessory genome.
Therefore we ask the question:
1) how does this diversity accumulate?
2) at what rate do genomes undergo large structural changes?
A thread 🧵 [1/13]
bert hubert 🇺🇦🇪🇺🇺🇦I'm a huge @duckdb fanboy, but even so it keeps amazing me. This is a 282 GB database of all bacterial genes & protein products. Here I ask DuckDB to find proteins *similar* to a specific one. It takes 9 seconds. Over 282GB w/o indexes.
bioRxiv BioinfoGlobal biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow https://www.biorxiv.org/content/10.1101/2024.05.04.592440v1?med=mas
Zeb LarsonOof, too true to academic life. https://www.mcsweeneys.net/articles/class-is-canceled-until-further-notice-while-i-do-my-job
MariaI think it is not difficult to understand that there are people with two surnames in academia.
Alex Crits-ChristophGenomeSPOT: Genome-based Salinity, pH, Oxygen Tolerance, and Temperature for Bacteria and Archaea
GitHub: https://github.com/cultivarium/GenomeSPOT
Preprint: https://www.biorxiv.org/content/10.1101/2024.03.22.586313v1
Axel ViselNice N&V Forum by @JakobWirbel, Ami Bhatt, Alexander Probst discussing how this study and the related Rodríguez del Río et al. provide insight into the vast structural and functional diversity of previously unknown microbial protein families
Christophe DessimozOur lab is excited to release FastOMA, a rewrite of OMA orthology algorithm that scales linearly, while maintaining OMA’s high accuracy. FastOMA can process all >2000 eukaryotic UniProt ref proteomes within 24 hours. Try it out https://github.com/DessimozLab/FastOMA
Preprint https://www.biorxiv.org/content/10.1101/2024.01.29.577392
Preprint https://www.biorxiv.org/content/10.1101/2024.01.29.577392
Stephen RoyleSeen on the other place.
I have been mystified why K represented Lysine for many years. Undergrad #biochemistry lecturer said “I don't know why, but I assume it is because of the end of the side chain looks like a K”. Well, turns out the answer is more simple.
Source: M Eugenio Vazquez. Posted in honour of Margaret Dayhoff, inventor of the single-letter amino acid code
