A comparative study of codon adaptation in ssDNA and dsDNA phages
Bibliographic record
Abstract
Selection and mutation are the main forces that shape the codon usage patterns of viruses. Bacteriophages, just like all other viruses depend on their host's translational machinery for replication. The rate of spontaneous C→T mutations is about 100-fold higher in single stranded DNA (ssDNA) than in double stranded DNA (dsDNA). We investigated the synonymous codon usage patterns of ssDNA phages and dsDNA phages to check if the two kinds of phages exhibit any difference in codon usage adaptation. We carried out relative synonymous codon usage (RSCU) analysis of 462 dsDNA phage and 41 ssDNA phage genomes with their respective bacterial hosts. Correlation in RSCU is significantly higher between dsDNA phages and their hosts than that between ssDNA phages and their hosts (p<0.005). Among the dsDNA phages we also found significant differences in codon adaptation between the three major phage families (p<0.0001).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 source (direct Gemma or distilled Codex), 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".