The Plant Orthology Browser: An Orthology and Gene‐Order Visualizer for Plant Comparative Genomics
Why this work is in the frame
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Bibliographic record
Abstract
Worldwide genome sequencing efforts for plants with medium and large genomes require identification and visualization of orthologous genes, while their syntenic conservation becomes the pinnacle of any comparative and functional genomics study. Using gene models for 20 fully sequenced plant genomes, including model organisms and staple crops such as Coss., (L.) Heynh., (L.) Beauv., turnip ( L.), barley ( L.), rice ( L.), sorghum [ (L.) Moench], wheat ( L.), red wild einkorn ( Tumanian ex Gandilyan), and maize ( L.), we computationally predicted 1,021,611 orthologs using stringent sequence similarity criteria. For each pair of plant species, we determined sets of conserved synteny blocks using strand orientation and physical mapping. Gene ontology (GO) annotations are added for each gene. Plant Orthology Browser (POB) includes three interconnected modules: (i) a gene-order visualization module implementing an interactive environment for exploration of gene order between any pair of chromosomes in two plant species, (ii) a synteny visualization module providing unique interactive dot plot representations of orthologous genes between a pair of chromosomes in two distinct plant species, and (iii) a search module that interconnects all modules via free-text search capability with online as-you-type suggestions and highlighting that allows exploration of the underlining information without constraint of interface-dependent search fields. The POB is a web-based orthology and annotation visualization tool, which currently supports 20 completely sequenced plant species with considerably large genomes and offers intuitive and highly interactive pairwise comparison and visualization of genomic traits via gene orthology.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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 it