Comparative Genomics Analysis of Enterocloster spp. Genomes for the Presence of ucd and uxd Operons
Bibliographic record
Abstract
Dataset for the analysis of Enterocloster spp. genomes for the presence/absence of ucd and uxd operons. Entry includes R code, RData, tables, FASTA queries (operon sequences), and Enterocloster spp. genomes from the NCBI genomes database. The results from the analysis are summarized in the operon_prevalence_by_accession_GTDB_sorted.csv file. General Methods: The analysis of ucd and uxd operon presence in Enterocloster spp. genomes was done by first downloading all available (n = 452) Enterocloster spp. genome sequences (FASTA format) from the NCBI genomes database (excluding atypical genomes) [https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=2719313&typical_only=true] (Accessed 01-08-2025). All FASTA files with GenBank GCA accessions were retained for further analysis (n = 452). The Genome Taxonomy Database (GTDB) table for Enterocloster spp. (release 10-RS226 (16-04-2025)) was downloaded from [https://gtdb.ecogenomic.org/searches?s=al&q=Enterocloster] (Accessed 02-08-2025). Each genome was queried using rBLAST (v1.2.0, DOI: 10.18129/B9.bioc.rBLAST) for matches to the E. bolteae ucd operon and E. asparagiformis uxd operon nucleotide sequences with criteria: -perc_identity 60 -max_target_seqs 5 -subject_besthit. Matches were further filtered for length > 300 bases to exclude small fragments. NCBI GenBank accessions for all queries without GTDB taxonomy or the "Undefined (Failed Quality Check)" flag were removed from further analyses, yielding a total of n = 329 genomes. Presence/absence of each operon was plotted in ggplot2 (v.3.5.2).
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.005 | 0.005 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".