AI Networking Cookbook: Practical recipes for AI-assisted network automation and development
TL;DR
A novel framework based on the Clusters of Orthologous Groups (COG) method, primarily designed for improving phylogenetic tree clustering in studying evolutionary history of eukaryotes, P-COGs (Pavlov's COGs).
The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution, and provides an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data.
It is demonstrated that most species-specific TRGs are genuine de novo gene births whereas most of the TRGs that are conserved across the Saccharomyces genus derive from highly diverged ancestral genes whose homology is no longer detectable using common methods.
A semi‐automated pipeline is developed and four genomic annotation methods (BRAKER2, BUSCO, Miniprot and Scipio) are compared to suggest that combining these tools can yield more accurate results in genomic research.
Over the past few years, the increasing interest in analyzing the proteome of extinct and nonmodel organisms has generated a new field of research expanding the scope of proteomics. The lack of curated databases and/or molecular data from these organisms forces researchers to manually search in different public reposit...
This chapter serves as a user-friendly practical tutorial for conducting structural phylogenetic analyses using accessible and computationally efficient tools, using synaptotagmins-calcium-sensing proteins essential for synaptic vesicle fusion-as a running example.
Where recombination takes place is crucial as it determines the position of genetic reshuffling, which facilitates species evolution and adaptation. In many vertebrates, PRDM9 determines the location of double-strand breaks that initiates meiotic recombination. However, this only applies for Prdm9 orthologs that posses...
We use cookies to run the site and, with your consent, for analytics and to show ads. See our Cookie Policy.