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.
The GenomeCompendium is released, a public database and interactive analysis tool for complete prokaryotic genomes and it is shown that complex, repeat-rich genomes are more common than previously estimated.
Tiberiu Totu, Garance Jaques, B. Heiniger et al.· bioRxiv· 0 citations
The ChlORIS database is presented, presenting a large-scale plastid phylogeny of 859 taxa spanning all major algal lineages and characterising the protein HMMs by cross-referencing them to Pfam domains and calibrated score cutoffs for reliable detection.
Yuhao Tong, Vanessa Rossetto Marcelino, Robert Turnbull et al.· bioRxiv· 0 citations
This study presents the first large-scale investigation of four prominent open-source annotation tools (Prokka, Bakta, EggNOG-mapper, and PGAP) across 156,033 diverse genomes, highlighting tool-specific strengths crucial for selecting optimal solutions based on genome quality, taxonomy, and origin.
Mateusz Jundzill, Martin Hölzer, S. Mangul et al.· Genome Biology· 0 citations
A novel operon prediction tool, DiscOperon, which combines gene expression data with homology searches to identify syntenic blocks in fully sequenced bacterial genomes using sequence homology searches, and is applied to predict the operons of M. xanthus.
Theo Brunet, Bianca H. Habermann· bioRxiv· 0 citations
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...
Guillermo Carrillo-Martin, Johanna Krueger, T. Marquès-Bonet et al.· Journal of Proteome Research· 0 citations
This work proposes a reproducible framework for analyzing the taxonomic structure of the nomen genus Stenotrophomonas and offers a reproducible framework for analyzing the taxonomic structure of the nomen genus Stenotrophomonas amid ongoing revisions.
V. Shapovalova, E. R. Shajdullina, G. Shipulin et al.· Clinical Microbiology and An...· 0 citations
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