KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences
Bibliographic record
Abstract
BACKGROUND: The volume of viral genomic sequence data continues to increase rapidly. This is especially true for the smaller RNA viruses, which are relatively easy to sequence in large numbers. The data volumes cause a number of significant problems for research applications that require large multiple alignments of essentially complete genomes, which are of the order of 10 kb. FINDINGS: We present a simple strategy to enable the creation of large quasi-multiple sequence alignments from pairwise alignment data. This process is suitable for large, closely related sequences such as the polyproteins of dengue viruses, which need the insertion of very few indels. CONCLUSION: The quasi-multiple sequence alignments generated by KISSa are sufficiently accurate to support tree-based genome selection for interactive bioinformatics analysis tools. The speed of this process is critical to providing an interactive experience for the user.
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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 | 0.005 | 0.013 |
| Meta-epidemiology (narrow) | 0.004 | 0.003 |
| Meta-epidemiology (broad) | 0.002 | 0.004 |
| Bibliometrics | 0.005 | 0.004 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.003 | 0.004 |
| Open science | 0.004 | 0.004 |
| Research integrity | 0.002 | 0.004 |
| Insufficient payload (model declined to judge) | 0.019 | 0.014 |
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".